Mishler's research interests can be grouped into two main areas: empirical studies of ecology, phylogeny, systematics, and development of mosses, and the theoretical basis of systematic and evolutionary biology.
Empirical studies include: (1) the phylogenetic relationships of the major groups of bryophytes (including mosses) and other land plants, using morphological, developmental, and ultrastructural characters as well as chloroplast DNA sequence data; (2) the development of moss peristomes in relation to evolution of the group; and (3) biosystematic studies of the haplolepideous mosses, including the tropical family Calymperaceae and the diverse temperate genus Tortula (Syntrichia), which involve transplant and ecological studies in the field, comparative physiological measurements and culture experiments in the lab, and morphological studies in the herbarium; (4) the reproductive biology of bryophytes, especially dryland mosses; and (5) the bryophyte floras of California, Moorea (in the Society Islands of the South Pacific), and Australia.
Theoretical studies include investigations of the nature of species, rank-free classification, methods for phylogenetic reconstruction (with an emphasis on cladistic analysis of molecular and genomic data), the relationship between development and evolution, phyloinformatics (comparative genomics, databasing, and visualization of phylogenetic trees), and biodiversity informatics (digitization of biological collections and integration with taxonomic and ecological data). His lab applies methods ranging from microscopy through growth experiments, DNA sequencing, and comparative genomics.
M. Benassi, L.R. Stark, J.C. Brinda, D.N. McLetchie, M. Bonine, and B.D. Mishler. 2011. Plant size, sex expression, and sexual reproduction along an elevation gradient in a desert moss. The Bryologist 114: 277-288.
B.D. Mishler. 2010. Species are not uniquely real biological entities. In F. Ayala and R. Arp (eds.), Contemporary Debates in Philosophy of Biology, pp. 110-122. Wiley-Blackwell
M.J. Oliver, A.G. Murdock, B.D. Mishler, J.V. Kuehl, J.L. Boore, D.F. Mandoli, K.D.E. Everett, P.G. Wolf, A.M. Duffy, and K.G. Karol. 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. http://www.ncbi.nlm.nih.gov/sites/ppmc/articles/PMC2841679/
K.G. Karol, K. Arumuganathan, J.L. Boore, A.M. Duffy, K.D.E. Everett, J.D. Hall, S.K. Hansen, J.V. Kuehl, D.F. Mandoli, B.D. Mishler, R.G. Olmstead, K.S. Renzaglia, and P.G. Wolf. 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. http://www.biomedcentral.com/1471-2148/10/321
B.D. Mishler and D.G. Kelch. 2009. Phylogenomics and early land plant evolution. In A.J. Shaw and B. Goffinet (eds.), Bryophyte Biology: Second Edition, pp. 173-197. Cambridge University Press.
B.D. Mishler. 2009. Three centuries of paradigm changes in biological classification: is the end in sight? Taxon 58: 61-67.
B.D. Mishler and M.J. Oliver. 2009. Putting Physcomitrella patens on the tree of life: the evolution and ecology of mosses. In C.D. Knight, P-F Peroud, and D.J. Cove (eds.), The Moss Physcomitrella patens. Annual Plant Reviews 36: 1-15. Wiley-Blackwell.
E.S.J. Harris and B.D. Mishler. 2009. The delimitation of phylogenetic characters. Biological Theory 4: 230-234.
S.A. Rensing, D. Lang, A.D. Zimmer, A. Terry, A. Salamov, H. Shapiro, T. Nishiyama, P-F. Perroud, E. Lindquist, Y. Kamisugi, T. Tanahashi, K. Sakakibara, T. Fujita, K. Oishi, T. Shin-I, Y. Kuroki, A. Toyoda, Y. Suzuki, S. Hashimoto, K. Yamaguchi, S. Sugano, Y. Kohara, A. Fujiyama, A. Anterola, S. Aoki, N. Ashton, W.B. Barbazuk, E. Barker, J.L. Bennetzen, R. Blankenship, S. H. Cho, S.K. Dutcher, M.Estelle, J.A. Fawcett, H. Gundlach, K. Hanada, A. Heyl, K.A. Hicks, J. Hughes, M. Lohr, K. Mayer, A. Melkozernov, T. Murata, D. Nelson, B. Pils, M. Prigge, B. Reiss, T. Renner, S. Rombauts, P. Rushton, A. Sanderfoot, G. Schween, S-H. Shiu, K. Stueber, F. L. Theodoulou, H. Tu, Y. Van de Peer, P. J. Verrier, E. Waters, A. Wood, L. Yang, D. Cove, A. C. Cuming, M. Hasebe, S. Lucas, B.D. Mishler, R. Reski, I.V. Grigoriev, R.S. Quatrano, and J.L. Boore. 2008. The Physcomitrella genome reveals evolutionary insights into the conquest of land by plants. Science 319: 64-69.
L.R. Stark, M.J. Oliver, B.D. Mishler, and D. N. McLetchie. 2007. Generational differences in response to desiccation stress in the desert moss Tortula inermis. Annals of Botany 99: 53-60.
K.M. Fisher, D.P. Wall, K.L. Yip, and B.D. Mishler. 2007. Phylogeny of the Calymperaceae with a rank-free systematic treatment. The Bryologist 110 (1): 46-73.
K.S. Renzaglia, S. Schuette, R.J. Duff, R. Ligrone, A.J. Shaw, B.D. Mishler, and J.G. Duckett. 2007. Bryophyte phylogeny: advancing the molecular and morphological frontiers. The Bryologist 110: 179-213. [with cover illustration]
B.D. Mishler. 2007. Syntrichia. In: Flora of North America Editorial Committee, eds. Flora of North America North of Mexico. Vol. 27, pp. 618-627.
M.C.F. Proctor, M.J. Oliver, A.J. Wood, P. Alpert, L.R. Stark, N.L. Cleavitt, and B.D. Mishler. 2007. Desiccation-tolerance in bryophytes: a review. The Bryologist 110: 595-621.