Shaw AJ, Duffy AM, Nieto-Lugilde M, Aguero B, Hassel K, Flatberg KI. 2026. Genomic and phylogenetic structure of the Sphagnum imbricatum complex (Sphagnaceae) and related alloploids. Annals of Botany mcag024, https://doi.org/10.1093/aob/mcag024.

Shaw AJ, Duffy AM, Aguero B, Nieto-Lugilde M, Imwattana K, Robinson SC, Schuette S, Wilkens RT, Yavitt J, Weston DJ, Piatkowski B, Granath G. 2025. Climate niches structure a regional hybrid zone in Sphagnum (peatmoss, Bryophyta). American Journal of Botany e70143.

Shaw AJ, Nieto-Lugilde M, Aguero B, Duffy AM, Robinson S, Hassel K, Flatberg KI, Ingerpuu N, Vellak K, Pérez-Haase A, Jiroušek M, Krebs M, Juselius-Rajamäki T, Piilo S, Robroek B, Lamkowski P, Granath G. 2025. Genetic structure of the Sphagnum magellanicum (Sphagnaceae) complex in Europe. The Bryologist 128(3):474–486.

Nieto-Lugilde M, Nieto-Lugilde D, Piatkowski B, Duffy AM, Robinson SC, Aguero B, Schuette S, Wilkens R, Yavitt J, Shaw AJ. 2024. Ecological differentiation and sympatry of cryptic species in the Sphagnum magellanicum complex (Bryophyta). American Journal of Botany 111(9):e16401.

Imwattana K, Aguero B, Nieto-Lugilde M, Duffy A, Jaramillo-Chico J, Hassel K, Afonina O, Lamkowski P, Shaw AJ. 2024. Parallel patterns of genetic diversity and structure in circumboreal species of the Sphagnum capillifolium complex. American Journal of Botany 111(5):e16348.

Robinson SC, Nieto-Lugilde M, Duffy AM, Muñoz KM, Aguero B, Merced A, Hassel K, Flatberg KI, Shaw AJ. 2024. The Sphagnum cuspidatum complex: phylogeny, species delimitation, and morphology. Biological Journal of the Linnean Society 141(4):466–492.

Piatkowski B, Weston DJ, Aguero B, Duffy A, Imwattana K, Healey AL, Schmutz J, Shaw AJ. 2023. Divergent selection and climate adaptation fuel genomic differentiation between sister species of Sphagnum (peat moss). Annals of Botany 132(3):499–512.

Shaw AJ, Duffy AM, Nieto-Lugilde M, Aguero B, Schuette S, Robinson S, Loveland J, Hicks KA, Weston D, Piatkowski B, Kolton M, Koska JE, Healey AL. 2023. Clonality, local population structure and gametophyte sex ratios in cryptic species of the Sphagnum magellanicum complex. Annals of Botany 132(1):77–94.

Shaw AJ, Nieto-Lugilde M, Aguero B, Duffy A, Piatkowski BT, Jaramillo-Chico J, Robinson S, Hassel K, Flatberg KI, Weston DJ, Schuette S, Hicks KA. 2023. Sphagnum diabolicum sp. nov. and S. magniae sp. nov.; morphological variation and taxonomy of the “S. magellanicum complex”. Bryologist 126(1):69–89.

Healey AL, Piatkowski B, Lovell JT, Sreedasyam A, Carey SB, Mamidi S, Shu S, Plott C, Jenkins J, Lawrence T, Aguero B, Carrell AA, Nieto-Lugilde M, Talag J, Duffy A, Jawdy S, Carter KR, Boston L-B, Jones T, Jaramillo-Chico J, Harkess A, Barry K, Keymanesh K, Bauer D, Grimwood J, Gunter L, Schmutz J, Weston DJ, Shaw AJ. 2023. Newly identified sex chromosomes in the Sphagnum (peat moss) genome alter carbon sequestration and ecosystem dynamics. Nature Plants 9(2):238–254.

Shaw, AJ, Piatkowski B, Duffy AM, Aguero B, Imwattana K, Nieto-Lugilde M, Healey A, Weston DJ, Patel MN, Schmutz J, Grimwood J, Yavitt JB, Hassel K, Stenøien HK, Flatberg KI, Bickford CP, Hicks KA. 2022. Phylogenomic structure and speciation in an emerging model: the Sphagnum magellanicum complex (Bryophyta). The New Phytologist 236(4):1497–1511.

Imwattana K, Aguero B, Duffy A, Shaw AJ. 2022. Demographic history and gene flow in the peatmosses Sphagnum recurvum and Sphagnum flexuosum (Bryophyta: Sphagnaceae). Ecology and Evolution 12(11):e9489.

Nieto-Lugilde M, Robinson S, Aguero B, Duffy A, Imwattana K, Hassel K, Flatberg KI, Stenøien HK, Shkurko AV, Fedosov VE, Shaw AJ. 2022. Morphological-molecular incongruence in Sphagnum majus ssp. majus and ssp. norvegicum. Bryologist 125(2):294–310.

Duffy AM, Ricca M, Robinson S, Aguero B, Johnson MG, Stenøien HK, Flatberg KI, Hassel K, Shaw AJ. 2022. Heterogeneous genetic structure in eastern North American peat mosses (Sphagnum). Biological Journal of the Linnean Society 135(4):692–707.

Duffy AM, Aguero B, Stenøien HK, Flatberg KI, Ignatov MS, Hassel K, Shaw AJ. 2020. Phylogenetic structure in the Sphagnum recurvum complex (Bryophyta) in relation to taxonomy and geography. American Journal of Botany 107(9):1283–1295.

Longhurst ML, Coster D, Wolf PG, Duffy AM, Lee H, Campbell T. 2016. Multi-year professional development grounded in educative curriculum focused on integrating technology with reformed science teaching principles. School Science and Mathematics 116:430–441.

Duffy AM, Stensvold MC, Farrar DR. 2015. Independent gametophytes of Hymenophllum wrightii in North America: not as rare as we thought. American Fern Journal 105:45–55.

Sessa EB, Banks JA, Barker MS, Der JP, Duffy AM, Graham SW, Hasebe M, Langdale J, Li F-W, Marchant DB, Pryer KM, Rothfels CJ, Roux SJ, Salmi ML, Sigel EM, Soltis DE, Soltis PS, Stevenson DW, Wolf PG. 2014. Between two fern genomes. GigaScience 3:15.

Schilling MP, Wolf PG, Duffy AM, Rai HS, Rowe CA, Richardson BA, Mock KE. 2014. Genotyping-by-sequencing for Populus population genomics: an assessment of genome sampling patterns and filtering approaches. PLoS One 9:e95292.

Duffy AM, Wolf PG, Barrow J, Longhurst M, Campbell T. 2013. Ecological investigations within an interactive plant community simulation. Science Scope 36:42–51.

Campbell T, Longhurst M, Duffy AM, Wolf PG, Shelton BE. 2013. Science teaching orientations and technology-enhanced tools for student learning. Research in Science Education 10.1007/s11165-012-9342-x

Campbell T, Longhurst M, Duffy AM, Wolf PG, Nagy R. 2012. Investigating human impact in the environment with faded scaffolded inquiry supported by technologies. Science Activities 49:99–107.

Liu H, Bowman M, Duffy AM, Hunt WA. 2012. Enabling behavior reuse in development of virtual environment applications. Proceedings of the 2012 Winter Simulation Conference, C Laroque, J Himmelspach, R Pasupathy, O Rose, and AM Uhrmacher, eds.

Clark JL, Funke MM, Duffy AM, Smith JF. 2012. Phylogeny of a Neotropical clade in the Gesneriaceae: more tales of convergent evolution. International Journal of Plant Sciences 173:894–916

Benninghoff AD, Orner GA, Buchner C, Hendricks JD, Duffy AM, Williams DE. 2012. Promotion of hepatocarcinogenesis by perfluoroalkyl acids in rainbow trout. Toxicological Sciences 125:69–78.

Karol KG, Arumuganathan K, Boore JL, Duffy AM, Everett KDE, Hall JD, Hansen SK, Kuehl JV, Mandoli DF, Mischler BD, Olmstead RG, Renzaglia KS, Wolf PG. 2010. Complete plastome sequences of Equisetum arvense and Isoetes flaccida: implications for phylogeny and plastid genome evolution of early land plant lineages. BMC Evolutionary Biology 10:321.

Wolf PG, Der JP, Duffy AM, Davidson JB, Grusz AL, Pryer KM. 2010. The evolution of chloroplast genes and genomes in ferns. Plant Molecular Biology 76: 251–261.

Campbell T, Wang SK, Hsu HY, Duffy AM, Wolf, PG. 2010. Learning with web tools, simulations, and other technologies in science classrooms. Journal of Science Education and Technology 19:505–511.

Wolf PG, Roper JM, Duffy AM. 2010. The evolution of chloroplast genome structure in ferns. Genome 53:731–738.

Oliver MJ, Murdock AG, Mishler BD, Kuehl JV, Boore JL, Mandoli DF, Everett KDE, Wolf PG, Duffy AM, Karol KG. 2010. Chloroplast genome sequence of the moss Tortula ruralis: gene content, polymorphism, and structural arrangement relative to other green plant chloroplast genomes. BMC Genomics 11:143.

Wolf PG, Duffy AM, Roper JM. 2009. Phylogenetic use of inversions in fern chloroplast genomes. American Fern Journal 99:132–134.

Duffy AM, Kelchner SA, Wolf PG. 2009. Conservation of selection on matK following an ancient loss of its flanking intron. Gene 438:17–25.

Presentations, Posters & Workshops:

Duffy, AM, Mendoza KM, Reed KM, Coulombe RA. Poster: Candidate miRNAs involved in regulation of alpha-class glutathione S-transferases associated with susceptibility to the carcinogen aflatoxin B1. Plant & Animal Genome Conference XXIV, San Diego, CA (2016).

Duffy AM, Farrar DR, Wolf PG. Presentation: Exploring the population genetics of independent gametophytes of Crepidomanes intricatum (Farrar) Ebihara & Weakley (Hymenophyllaceae) using genotyping-by-sequencing. Botany 2014, Boise, ID (2014).

Duffy AM. Workshop: Hands-on inquiry using the Virtual Plant Community Simulation (VPCsim). Utah State University Global Academy—Science, Technology and Inquiry session, Logan, UT (2012).

Duffy AM, Campbell T, Wolf PG. Workshop: The Virtual Population Genetics (VPG) Simulation System: An example of learning ‘with’ cyber-enabled technologies in science classrooms. National Science Teachers Association Research Dissemination Conference, San Francisco, CA (2011).

Campbell T, Duffy AM. Workshop: OpenSim as an example of cyber-enabled technologies for facilitating science as inquiry. Cyberlearning Tools for STEM Education Conference, Berkeley, CA (2011).

Duffy AM. Presentation: Simulating fern life cycles and population genetics in a 3-dimensional virtual world. Botany 2009, Snowbird, UT and Idaho State University Practical Bioinformatics Workshop, Lava Hot Springs, ID (2009).

Duffy AM, Kelchner SA, Wolf PG. Presentation: Conservation of selection on matK in ferns following an ancient loss of the trnK intron by genome inversion. Botany 2008, Vancouver, BC and Idaho State University Practical Bioinformatics Workshop, Lava Hot Springs, ID (2008).

Duffy AM, Funke MM, Clark JL, Smith JF. Presentation: A phylogenetic analysis of the genera of tribe Episcieae (Gesneriaceae) from multiple loci. Botany 2004, Snowbird, UT and Northwest Science Association, Boise, ID (2006).

Duffy AM, Funke MM, Clark JL, Smith JF. Poster: A phylogenetic analysis of the genera of tribe Episcieae (Gesneriaceae) from multiple loci. BSU Day at the Legislature, Idaho State Capitol, Boise ID (2005), and BSU Undergraduate Research and Scholarship Conference, Boise, ID (2005).