Joshua P. Der

Contact Information

Office: MH 640A

Phone: 657-278-4115


Joshua P. Der

Assistant Professor


PhD, Utah State University

MS, Southern Illinois University, Carbondale

BS, Humboldt State University

Research Areas

Plant evolutionary genomics, plant systematics, bioinformatics, and molecular evolution. Evolution of life history transitions in parasitic plants (esp. mistletoes) and land plants (esp. ferns).

Courses Regularly Taught

BIOL 152 - Evolution and Biodiversity, BIOL 325 - Principles of Evolution, BIOL 410 - Evolutionary Genetics, BIOL 441 - Plant Taxonomy


Honaas, L. A., Wafula, E. K., Wickett, N. J., Der, J. P., Zhang, Y., Edger, P. P., Altman, N. S., Pires, J. C., Leebens-Mack, J. H., dePamphilis, C. W. (2016) Selecting Superior De Novo Transcriptome Assemblies: Lessons Learned by Leveraging the Best Plant Genome. PLoS ONE, 11(1), e0146062. DOI: 10.1371/journal.pone.0146062.

Naumann, J., Der, J. P., Wafula, E. K., Jones, S. S., Wagner, S. T., Honaas, L. A., Ralph, P. E., Bolin, J. F., Maass, E., Neinhuis, C., Wanke, S., dePamphilis, C. W. (2016). Detecting and characterizing the highly divergent plastid genome of the nonphotosynthetic parasitic plant Hydnora visseri (Hydnoraceae). Genome Biology and Evolution, 8(1), evv256. DOI: 10.1093/gbe/evv256.

Medved, V., Marden, J. H., Fescemyer, H. W., Der, J. P., Liu, J., Mahfooz, N., Popadic, A. Origin and diversification of wings: insights from a neopteran insect. Proceedings of the National Academy of Sciences USA, 112(52), 15946-15951.

Wolf P. G., Rowe C. A., Der J. P., Schilling M. P., Visger C. J., Thomson J. A. (2015) Origins and diversity of a cosmopolitan fern genus on an island archipelago. AoB Plants, 7(1), plv118. DOI: 10.1093/aobpla/plv118.

Wolf, P. G., Sessa, E. B., Marchant, D. B., Li, F.-W., Rothfels, C. J., Sigel, E. M., Gitzendanner, M. A., Visger, C. J., Banks, J. A., Soltis, D. E., Soltis, P. S., Pryer, K. M., & Der, J. P. (2015) An exploration into fern genome space. Genome Biology and Evolution, 7(9), 2533-2544. DOI: 10.1093/gbe/evv163.

Edger, P., Heidel-Fischer, H. M., Bekaert, M., Rota, J., Glöckner, G., Platts, A. E., Heckel, D. G., Der, J. P., Wafula, E. K., Tang, M., Hofberger, J., Smithson, A., Hall, J., Blanchette, M., Bureau, T., Wright, S., dePamphilis, C. W., Schranz, M. E., Barker, M., Conant, G. C., Wahlberg, N., Vogel, H., Pires, J. C., & Wheat, C. W. (2015). The butterfly plant arms-race escalated by gene and genome duplications. Proceedings of the National Academy of Sciences USA, 112(27), 8362-8366. DOI: 10.1073/pnas.1503926112.

Su, H.-J., Hu, J.-M., Anderson, F. E., Der, J. P., & Nickrent, D. L. (2015). Phylogenetic relationships of Santalales with insights into the origins of holoparasitic Balanophoraceae. Taxon, 64(3), 491-506. DOI: 10.12705/643.2.

Yang, Z., Wafula, E. K., Honaas, L. A., Zhang, H., Das, M., Fernandez-Aparicio, M., Huang, K., Bandaranayake, P. C. G., Wu, B., Der, J. P., Clarke, C. R., Ralph, P. E., Landherr, L., Altman, N. S., Timko, M. P., Yoder, J. I., Westwood, J. H., & dePamphilis, C. W. (2015). Comparative transcriptome analyses reveal core parasitism genes and suggest gene duplication and repurposing as sources of structural novelty. Molecular Biology and Evolution, 32(1), 767-790. DOI: 10.1093/molbev/msu343.

Wickett N.J., Mirarab S., Nguyen N., Warnow T., Carpenter E., Matasci N., Ayyampalayam S., Barker M.S., Burleigh J.G., Gitzendanner M.A., Ruhfel B.R., Wafula E., Der J.P., Graham S.W., Mathews S., Melkonian M., Soltis D.E., Soltis P.S., Miles N.W., Rothfels C.J., Pokorny L., Shaw A.J., DeGironimo L., Stevenson D.W., Surek B., Villarreal J.C., Roure B., Philippe H., dePamphilis C.W., Chen T., Deyholos M.K., Baucom R.S., Kutchan T.M., Augustin M.M., Wang J., Zhang Y., Tian Z., Yan Z., Wu X., Sun X., Wong G.K.-S., Leebens-Mack J. 2014. Phylotranscriptomic analysis of the origin and early diversification of land plants. P Natl Acad Sci USA. 111:E4859–68.

Matasci N., Hung L.-H., Yan Z., Carpenter E.J., Wickett N.J., Mirarab S., Nguyen N., Warnow T., Ayyampalayam S., Barker M., Burleigh J., Gitzendanner M.A., Wafula E., Der J.P., dePamphilis C.W., Roure B., Philippe H., Ruhfel B.R., Miles N.W., Graham S.W., Mathews S., Surek B., Melkonian M., Soltis D.E., Soltis P.S., Rothfels C., Pokorny L., Shaw J.A., DeGironimo L., Stevenson D.W., Villarreal J., Chen T., Kutchan T.M., Rolf M., Baucom R.S., Deyholos M.K., Samudrala R., Tian Z., Wu X., Sun X., Zhang Y., Wang J., Leebens-Mack J., Wong G.K.-S. 2014. Data access for the 1,000 Plants (1KP) project. GigaScience. 3:17.

Sessa E.B., Banks J.A., Barker M.S., Der J.P., Duffy A.M., Graham S.W., Hasebe M., Langdale J., Li F.-W., Marchant D.B., Pryer K.M., Rothfels C.J., Roux S.J., Salmi M.L., Sigel E.M., Soltis D.E., Soltis P.S., Stevenson D.W., Wolf P.G. 2014. Between Two Fern Genomes. GigaScience. 3:15.

Li F.-W., Villarreal J.C., Kelly S., Rothfels C.J., Melkonian M., Frangedakis E., Ruhsam M., Sigel E.M., Der J.P., Pittermann J., Burge D.O., Pokorny L., Larsson A., Chen T., Weststrand S., Thomas P., Carpenter E., Zhang Y., Tian Z., Chen L., Yan Z., Zhu Y., Sun X., Wang J., Stevenson D.W., Crandall-Stotler B.J., Shaw A.J., Deyholos M.K., Soltis D.E., Graham S.W., Windham M.D., Langdale J.A., Wong G.K.-S., Mathews S., Pryer K.M. 2014. Horizontal transfer of an adaptive chimeric photoreceptor from bryophytes to ferns. P Natl Acad Sci USA. 111:6672–6677.

Williams J.S., Der J.P., dePamphilis C.W., Kao T.-H. 2014. Transcriptome Analysis Reveals the Same 17 S-Locus F-Box Genes in Two Haplotypes of the Self-Incompatibility Locus ofPetunia inflata. Plant Cell. 26:2873–2888.

McCarthy T.W., Der J.P., Honaas L.A., dePamphilis C.W., Anderson C.T. 2014. Phylogenetic analysis of pectin-related gene families in Physcomitrella patens and nine other plant species yields evolutionary insights into cell walls. BMC Plant Biol. 14:79.

Amborella Genome Project. 2013. The Amborella genome and the evolution of flowering plants. Science. 342:1241089.

Chamala S., Chanderbali A.S., Der J.P., Lan T., Walts B., Albert V.A., dePamphilis C.W., Leebens-Mack J., Rounsley S., Schuster S.C., Wing R.A., Xiao N., Moore R., Soltis P.S., Soltis D.E., Barbazuk W.B. 2013. Assembly and validation of the genome of the nonmodel basal angiosperm Amborella. Science. 342:1516–1517.

Naumann J., Salomo K., Der J.P., Wafula E.K., Bolin J.F. 2013. Single-Copy Nuclear Genes Place Haustorial Hydnoraceae within Piperales and Reveal a Cretaceous Origin of Multiple Parasitic Angiosperm Lineages. PLoS ONE. 8(11):e79204.

Ming R., VanBuren R., Liu Y., Yang M., Han Y., Li L.-T., Zhang Q., Kim M.-J., Schatz M.C., Campbell M., Li J., Bowers J.E., Tang H., Lyons E., Ferguson A.A., Narzisi G., Nelson D.R., Blaby-Haas C.E., Gschwend A.R., Jiao Y., Der J.P., Zeng F., Han J., Min X.J., Hudson K.A., Singh R., Grennan A.K., Karpowicz S.J., Watling J.R., Ito K., Robinson S.A., Hudson M.E., Yu Q., Mockler T.C., Carroll A., Zheng Y., Sunkar R., Jia R., Chen N., Arro J., Wai C.M., Wafula E., Spence A., Han Y., Xu L., Zhang J., Peery R., Haus M.J., Xiong W., Walsh J.A., Wu J., Wang M.-L., Zhu Y.J., Paull R.E., Britt A.B., Du C., Downie S.R., Schuler M.A., Michael T.P., Long S.P., Ort D.R., William Schopf J., Gang D.R., Jiang N., Yandell M., dePamphilis C.W., Merchant S.S., Paterson A.H., Buchanan B.B., Li S., Shen-Miller J. 2013. Genome of the long-living sacred lotus (Nelumbo nucifera Gaertn.). Genome Biol. 14:R41.

Honaas L.A., Wafula E.K., Yang Z., Der J.P., Wickett N.J., Altman N.S., Taylor C.G., Yoder J.I., Timko M.P., Westwood J.H., dePamphilis C.W. 2013. Functional genomics of a generalist parasitic plant: laser microdissection of host-parasite interface reveals host-specific patterns of parasite gene expression. BMC Plant Biol. 13:9.

Campbell T., Der J.P., Wolf P.G., Packenham E., Abd-Hamid N.H. 2012. Scientific Inquiry in the Genetics Laboratory: Biologists and University Science Teacher Educators Collaborating to Increase Engagement in Science Processes. Journal of College Science Teaching. 41:74–81.

Der J.P., Barker M.S., Wickett N.J., dePamphilis C.W., Wolf P.G. 2011. De novo characterization of the gametophyte transcriptome in bracken fern, Pteridium aquilinum. BMC Genomics. 12:99.

Wolf P.G., Der J.P., Duffy A.M., Davidson J.B., Grusz A.L., Pryer K.M. 2011. The evolution of chloroplast genes and genomes in ferns. Plant Mol Biol. 76:251–261.

Nickrent D.L., Malécot V., Vidal-Russell R., Der J.P. 2010. A revised classification of Santalales. Taxon. 59:538–558.