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Dr. Joseph Nairn

Professor, Conservation Genetics, Molecular Ecology, Forest Biotechnology

Contact Information

Pictured: Dr. Joe Nairn

Contact Dr. Joseph Nairn


Campus address

Warnell 3-211
Lab Location:
Warnell 3-202 & 3-205
Ph.D. Major-Molecular Biology/Plant Science, Minor-Zoology, University of Florida
M.S. Molecular Biology/Botany, University of Florida
B.S. Biology, University of Central Florida


Research Areas Detail:

The overarching goal of our research program is to conduct basic and applied research focused on conservation, management, and restoration of natural resources. Molecular genetic and genomic approaches, as well as other biotechnologies are central to our program. Projects in the lab include two somewhat distinct, but complimentary areas of research. 

The first of these is focused on the genetics of wildlife populations, particularly threatened species. The current rate at which species are disappearing or declining is of great concern. Additionally, fragmentation of habitat and populations restricts migration, dispersal and consequently gene flow. We use molecular genetics and genomic approaches to study these populations. Research topics include genetic structure, differentiation between fragmented populations, and inbreeding in small populations. Ongoing projects include the genetic structure of marine turtle populations in the southeastern US and the Greater Caribbean and the reproductive ecology of loggerhead turtles in the US Northern Recovery Unit. Collaborations with marine turtle researchers from around the globe combine data from individual efforts to investigate genetic structure and ecology of marine turtles across ocean basins and on a global scale. 

A second area of emphasis in the lab is Forest Biotechnology. We have characterized genes involved in cellulose and hemicellulose synthesis of loblolly pine and approaches for modifying properties of lignocellulosic feedstocks for bioenergy production. Current research includes forest health, particularly emerging threats to natural forests that are frequently due to introduced pathogens. We collaborate with Dr. Scott Merkle’s research group on American chestnut restoration. A major objective of this work is to identify and propagate American chestnut germplasm with resistance to the chestnut blight Cryphonectriaand root diseases caused by Phytophthora. We accept graduate students for M.S. and PhD. programs of study in the fall semester. Graduate assistantships are available on a competitive basis to qualified candidates. Applications are generally due in January for admission in the fall semester. Application and program details can be found at

Prior Positions:
University of Georgia, Department of Plant Biology, Assistant Research Scientist
University of Florida, Department of Horticultural Sciences, Research Associate
U.S.D.A. ,A.R.S., Horticultural Research Laboratory, Research Scientist

Recent Citations:

Naro-Maciel, E., Reid, B.N., Alter, S.E., Amato, G., Bjorndal, K.A., Bolten, A.B., Martin, M., Nairn, C.J., Shamblin, B., Pineda-Catalan, O. (2014) From refugia to rookeries: Phylogeography of Atlantic green turtles. Journal of Experimental Marine Biology and Ecology 461:306-316.

Kong, L., Holtz, C.T., Nairn, C.J., Houke, H., Powell, W.A., Baier, K., Merkle, S.A. (2014) Application of airlift bioreactors to accelerate genetic transformation in American chestnut. Plant Cell Tissue and Organ Culture 117:39-50.

Shamblin BM, Bolten AB, Abreu-Grobois FA, Bjorndal KA, Cardona L, Carreras C, Clusa M, Monzón-Argüello C, Nairn CJ, Nielsen JT, Nel R, Soares LS, Stewart KR, Vilaça ST, Türkozan O, Yilmaz C, Dutton PH (2014) Geographic patterns of genetic variation in a broadly distributed marine vertebrate: new insights into loggerhead turtle stock structure from expanded mitochondrial DNA sequences. PLoS ONE 9(1): DOI:10.1371/journal.pone.0085956

Vander Zanden H.B., Pfaller J.B., Reich K.J., Pajuelo M., Bolten A.B., Williams K.L., Frick M.G., Shamblin B.M., Nairn C.J., Bjorndal K.A. (2014) Foraging areas differentially affect reproductive output and interpretation of trends in abundance of loggerhead turtles. Marine Biology 161:585-598.

Shamblin, B.M., Bjorndal, K.A., Bolten, A.B., Nairn, C.J. (2012) Natal homing by an adult male green turtle at Tortuguero, Costa Rica. Marine Turtle Newsletter 134:21-22.

Shamblin, B.M., Bolten, A.B., Bjorndal, K.A., Dutton, P.H., Nielsen, J.T., Abreu-Grobois, A., Reich, K.J., Witherington, B.E., Bagley, D.A., Ehrhart, L.M., Tucker, A.D., Addison, D.S., Arenas, A., Johnson, C., Carthy, R.R., Lamont, M.M., Dodd, M.G., Gaines, M.S., LaCasella, E., Nairn, C.J. (2012) Expanded mitochondrial control region sequences increase resolution of stock structure among North Atlantic loggerhead turtle rookeries. Marine Ecology Progress Series 469:145-160.

Lehmicke, A.J., Berry, B.E., Shamblin, B.M., Lennon, D.M., Woodrey, M.S., Cooper, R.J., Nairn, C.J. (2012) Isolation and charactertization of tetranucleotide microsatellite loci from the seaside sparrow (Ammodramus maritimus). Conservation Genetics Resources 4:881-884.

Shamblin, B.M., Bjorndal, K.A., Bolten, A.B., Hillis-Starr, Z.M., Lundgren, I., Naro-Maciel, E., Nairn, C.J. (2012) Mitogenomic sequences better resolve stock structure of southern Greater Caribbean green turtle rookeries. Molecular Ecology 21:2330-2340.

Shamblin, B.M., Dodd, M.G., Bagley, D.A., Ehrhart, L.M., Tucker, A.D., Johnson, C., Carthy, R.R., Scarpino, R.A., McMichael, E., Addison, D.S., Williams, K.L., Frick, M.G., Ouellette, S., Meylan, A.B., Godfrey, M.H., Murphy, S.R., Nairn, C.J. (2011) Genetic structure of the southeastern United States loggerhead turtle nesting aggregation: evidence of additional structure within the peninsular Florida recovery unit. Marine Biology158:571-587.

Shamblin, B.M., Dodd, M.G., Williams, K.L., Frick, M.G., Bell, R., Nairn, C.J. (2011) Loggerhead turtle eggshells as a source of maternal nuclear genomic DNA for population genetic studies. Molecular Ecology Resources 11:110-115.

Alstad, T.I., Shamblin, B.M., Warren, R.J., Stober, J.M., Conner, L.M., Cooper, R.J., Nairn, C.J. (2009) Novel tetranucleotide and pentanucleotide microsatellite loci in the red-cockaded woodpecker (Picoides borealis). Conservation Genetics Resources 1:213-215.

Liu, A.Z., Samils N., Higgins, B., Stenlid, J., Slippers, B., Nairn, C.J., Covert, S.F. (2009) Microsatellite markers for the wood decay fungus Phlebiopsis giganteaConservation Genetics 10:1529-1532.

Andrade, G.M., Nairn, C.J., Le, H.T., Merkle, S.A. (2009) Sexually mature transgenic American chestnut trees via embryogenic suspension-based transformation. Plant Cell Reports 28:1385-1397.

Nairn, C.J., Lennon, D.M., Wood-Jones, A., Nairn, A.V., Dean, J.F.D. (2008) Carbohydrate-Related Genes and Cell Wall Biosynthesis in Vascular Tissues of Loblolly Pine (Pinus taeda L.). Tree Physiology28:1099-1110.

Merkle, S.A., Andrade, G.M., Nairn, C.J., Powell, W.A., Maynard, C.A. (2007) Restoration of Threatened Species: A Noble Cause for Transgenic Trees. Tree Genetics and Genomes 3:111-118.

Liepman, A.H., Nairn, C. J., Willats, W.G.T., Sørensen, I., Roberts, A.W., Keegstra, K. (2007) Functional genomic analysis supports conservation of function among CslA gene family members and highlights diverse roles of mannans in plants. Plant Physiology143:1881-1893.

Polin, L.D., Liang, H., Rothrock, R.E., Nishii, M., Diehl, D.L., Newhouse, A.E., Nairn, C.J., Powell, W.A., Maynard, C.A. (2006) Agrobacterium-mediated transformation of American Chestnut (Castanea dentata (Marsh.) Borkh.) somatic embryos. Plant Cell, Tissue & Organ Culture 84: 69-78.

Zhou, G-K., Zhong, R., Richardson, E.A., Morrison, W.H.III, Nairn, C.J., Wood-Jones, A., Ye, Z-H. (2006) The poplar glycosyltransferase GT47C is functionally conserved with Arabidopsis Fragile Fiber8Plant and Cell Physiology 47: 1229-1240.

Joshi, M., Niu, C., Fleming, G., Hazra, S., Chu, Y., Nairn, C.J., Yang, H., Ozias-Akins, P. (2005) Use of green fluorescent protein as a non-destructive marker for peanut genetic transformation. In Vitro Cell. Dev. Biol. – Plant 41:437-445.

Zhong, R., Burk, D.H., Nairn, C.J., Wood-Jones, A., Morrison, W.H. III, Ye, Z.H. (2005) Mutation of SAC1, an Arabidopsis SAC Domain Phosphoinositide Phosphatase, Causes Alterations in Cell Morphogenesis, Cell Wall Synthesis, and Actin Organization. Plant Cell 17:1449-1466.

Nairn, C.J., Haselkorn, T. (2005) Three loblolly pine CesA genes expressed in developing xylem are orthologous to secondary cell wall CesA genes of angiosperms. New Phytologist 166:907-915.

Merkle, S.A., Nairn, C.J. (2005) Hardwood tree biotechnology. In Vitro Cell. Dev. Biol. – Plant41:602-619.

Zhong, R., Pena, M.J., Zhou, G.K., Nairn, C.J., Wood-Jones, A., Richardson, E.A., Morrison, W.H.III, Darvill, A.G., York, W.S., Ye, Z.H. (2005) Arabidopsis Fragile Fiber8, which encodes a putative glucuronyltransferase, is essential for normal secondary wall synthesis. Plant Cell17:3390-3408.

Yang, H., Nairn, C. J., Ozias-Akins, P. (2003) Transformation of peanut using a modified bacterial mercuric ion reductase gene driven by an actin promoter from Arabidopsis thaliana.  Journal of Plant Physiology 160:945-952.