Shi T, Gugger PF, Wang M-H, Li H, Li Z-Z, Liu Y-L, Wang Q-F, Chen J-M (Submitted) Genomic relics from ancestral angiosperm and lineage-specific genome duplications in the conserved lotus genome. Molecular Biology and Evolution.

Garner M, Pham K, Whittemore AT, Cavender-Bares J, Gugger PF, Manos PS, Pearse IS, Hipp AL (Submitted) From Manitoba to Texas: A study of the population genetic structure of bur oak (Quercus macrocarpa). International Oaks.

Hipp AL, Whittemore AT, Garner M, Hahn M, Fitzek E, Guichoux E, Cavender-Bares J, Gugger PF, Manos PS, Pearse IS, Cannon CH (Submitted) The Eastern North America white oak syngameon is made up of genetically cohesive species. Annals of the Missouri Botanical Garden.

Meng H-H, Zhou S-S, Jiang X-L, Gugger PF, Li L, Tan H-T, Li J (Submitted) Are mountaintops climate refugia for plants under global warming? A lesson from high-mountain oaks in tropical rainforest. Journal of Systematics and Evolution.


Zhao J-L, Werth S, Ikegami M, Gugger PF, Sork VL (2019) Historical interactions are predicted to be disrupted under future climate change: the case of lace lichen and valley oak. Journal of Biogeography, 46(1):19-29, doi:10.1111/jbi.13442.

Albarrán-Lara AL, Petit RJ, Kremer A, Caron H, Peñaloza-Ramírez JM, Gugger PF, Dávila-Aranda PD, Oyama K (2019) Limited genetic differentiation between two morphologically and ecologically distinct giant-leaved Mexican oaks. Plant Systematics and Evolution, 305(1):89-101, doi:10.1007/s00606-018-1554-8.


Gugger PF, Liang CT, Sork VL, Hodgskiss P, Wright JW (2018) Applying landscape genomic tools to forest management and restoration of Hawaiian koa (Acacia koa) in a changing environment. Evolutionary Applications, 11(2):231-242,  doi:10.1111/eva.12534.

Martins K, Gugger PF, Llanderal-Mendoza J, González-Rodríguez A, Fitz-Gibbon S, Zhao J-L, Oyama K, Sork VL (2018) Landscape genomics provides evidence of climate-associated adaptive genetic variation in Mexican populations of Quercus rugosa. Evolutionary Applications, 11:1842–1858, doi:10.1111/eva.12684.

Ortego J, Gugger PF, Sork VL (2018) Genomic data reveal cryptic lineage diversification and introgression in Californian golden cup oaks (section Protobalanus). New Phytologist, 218(2):804–818, doi:10.1111/nph.14951.

Evans MEK, Gugger PF, Lynch AM, Guiterman CH, Fowler JC, Klesse S, Riordin EC (2018) Dendroecology meets genomics in the common garden: new insights into climate adaptation. New Phytologist, 218(2):401–403, doi:10.1111/nph.15094.

Kim BY, Wei X-Z, Fitz-Gibbon ST, Lohmueller KE, Ortego J, Gugger PF, Sork VL (2018) RADseq data reveal ancient, but not pervasive, introgression among Californian tree and scrub oak species (Quercus: Fagaceae). Molecular Ecology, 27(22):4556–4571, doi:10.1111/mec.14869.

Öney-Birol S, Fitz-Gibbon ST, Chen J-M, Gugger PF, Sork VL (2018) Assessment of shared alleles in drought-associated candidate genes among southern California white oak species (Quercus sect. Quercus). BMC Genetics, 19:88, doi:10.1186/s12863-018-0677-9.

Nelson DM, Nagel J, Trott R, Campbell CJ, Pruitt L, Good RE, Iskali G, Gugger PF (2018) Carcass age and searcher identity affect morphological assessment of the sex of bats. Journal of Wildlife Management, 82(8):1582–1587, doi:10.1002/jwmg.21544.

Butler-Leopold PR, Iverson LR, Thompson III FR, Brandt LA, Handler SD, Janowiak MK, Shannon PD, Swanston C, Bearer S, Bryan AM, Clark KL, Czarnecki G, DeSenze P, Dijak WD, Fraser J, Gugger PF, et al. (2018) Mid-Atlantic Forest Ecosystem Vulnerability Assessment and Synthesis: a report from the Mid-Atlantic Climate Change Response Framework. General Technical Report NRS-GTR-181. Newtown Square, PA; U.S. Department of Agriculture, Forest Service, Northern Research Station, 294 p. doi:10.2737/NRS-GTR-18.

He D, Guo P, Gugger PF, Guo Y, Liu X, Chen J-M (2018) Investigating the molecular basis for heterophylly in the aquatic plant Potamogeton octandrus (Potamogetonaceae) with comparative transcriptomics. PeerJ, 6:e4448, doi:10.7717/peerj.4448.


Gugger PF*, Peñaloza-Ramírez JM*, Wright JW, Sork VL (2017) Whole-transcriptome response to water stress in a California endemic oak, Quercus lobata. Tree Physiology, 37(5):632–644, doi:10.1093/treephys/tpw122.  *equal contributors

Ortego J, Gugger PF, Sork VL (2017) Impacts of human-induced environmental disturbances on hybridization between two ecologically differentiated Californian oak species. New Phytologist, 213(2):942–955, doi:10.1111/nph.14182.

Llanderal-Mendoza J, Gugger PF, Oyama K, Uribe-Salas D, González-Rodríguez A (2017) Climatic determinants of acorn size and germination rate of Quercus rugosa (Fagaceae) along a latitudinal gradient. Botanical Sciences, 95(1):37–45, doi:10.17129/botsci.640.

Fetter K, Gugger PF, Keller SR (2017) Landscape genomics of angiosperm trees: from historic roots to discovering new branches of adaptive evolution. In: Groover A, Cronk Q (Eds.) Comparative and Evolutionary Genomics of Angiosperm Trees (pp. 303–333). Springer, Cham, Switzerland, doi:10.1007/7397_2016_19.

Dudley N, Jones T, James R, Sniezko R, Wright J, Liang C, Gugger PF, Cannon P (2017) Applied genetic conservation of Hawaiian Acacia koa: an eco-regional approach. In Sniezko RA, Man G, Hipkins V, Woeste K, Gwaze D, Kliejunas JT, McTeague BA (Tech. cords.), Gene conservation of tree species–banking on the future. Proceedings of a workshop (pp. 78–91). General Technical Report PNW-GTR-963. USDA Forest Service, Pacific Northwest Research Station, Portland, OR. [Abstract] [PDF]


Gugger PF, Fitz-Gibbon S, Pellegrini M, Sork VL (2016) Species-wide patterns of DNA methylation variation in Quercus lobata and their association with climate gradients. Molecular Ecology, 25(8):1665–1680, doi:10.1111/mec.13563.

Gugger PF, Cokus SJ, Sork VL (2016) Association of transcriptome-wide sequence variation with climate gradients in valley oak (Quercus lobata). Tree Genetics & Genomes, 12(2):15, doi:10.1007/s11295-016-0975-1.

Sork VL, Gugger PF, Chen J-M, Werth S (2016) Evolutionary lessons from California plant phylogeography. Proceedings of the National Academy of Sciences, 113(29):8064–8071, doi:10.1073/pnas.1602675113.

Sork VL, Fitz-Gibbon ST, Puiu D, Crepau MW, Gugger PF, Sherman R, Stevens K, Langley CH, Pellegrini M, Salzberg SL (2016) First draft assembly and annotation of the genome of a California endemic oak, Quercus lobata Née (Fagaceae). G3: Genes, Genetics, Genomes, 6(11):3485–3495, doi:10.1534/g3.116.030411.

Sork VL, Squire K, Gugger PF, Levy E, Steele S, Eckert AJ (2016) Landscape genomic analysis of candidate genes for climate adaptation in a California endemic oak, Quercus lobata Née (Fagaceae). American Journal of Botany, 103(1):33–46, doi:10.3732/ajb.1500162.

Riordan EC, Gugger PF, Ortego J, Smith C, Gaddis K, Thompson P, Sork VL (2016) Association of genetic and phenotypic variability with geography and climate in three southern California oaks. American Journal of Botany, 103(1):73–85, doi:10.3732/ajb.1500135.

Zhao J-L, Gugger PF, Xia Y-M, Li Q-J (2016) Ecological divergence of two closely related Roscoea species associated with late Quaternary climate change. Journal of Biogeography, 43(10):1990–2001, doi:10.1111/jbi.12809.

Sork VL, Ortego J, Riordan E, Gugger PF, Fitz-Gibbon S, Wei X (2016) Phylogeny and introgression of California scrub white oaks (Quercus sect. Quercus). International Oaks, 27:61–74.

Sun S-S, Gugger PF, Wang Q-F, Chen J-M (2016) Identification of a R2R3-MYB gene regulating anthocyanin biosynthesis and relationships between its variation and flower color difference in lotus (Nelumbo Adans.). PeerJ, e2369, doi:10.7717/peerj.2369.


Cokus SJ*, Gugger PF*, Sork VL (2015) Evolutionary insights from de novo transcriptome assembly and SNP discovery in California white oaks. BMC Genomics, 16:552, doi:10.1186/s12864-015-1761-4.  *equal contributors

Platt A, Gugger PF, Pellegrini M, Sork VL (2015) Genome-wide signature of local adaptation linked to variable CpG methylation in oak populations. Molecular Ecology, 24(15):3823–3830, doi:10.1111/mec.13230. [Commentary]

Ortego J, Gugger PF, Sork VL (2015) Climatically stable landscapes predict patterns of genetic structure and admixture in the Californian canyon live oak. Journal of Biogegraphy, 42(2):328–338, doi:10.1111/jbi.12419.

Ortego J, Noguerales V, Gugger PF, Sork VL (2015) Evolutionary and demographic history of the Californian scrub white oak species complex: an integrative approach. Molecular Ecology, 24: 6188–6208, doi:10.1111/mec.13457.

Delfino-Mix A, Wright JW, Gugger PF, Liang CF, Sork VL (2015) Establishing a range-wide provenance test in valley oak (Quercus lobata Née) at two California sites. In: Proceedings of the seventh oak symposium: managing oak woodlands in a dynamic world. USDA Forest Service General Technical Report PSW-GTR-251, 413–424. [Abstract] [PDF]

Albarrán-Lara AL, Wright JW, Gugger PF, Delfino-Mix A, Peñaloza-Ramírez JM, Sork VL (2015) Phenotypic variation in California populations of valley oak (Quercus lobata Née) sampled along elevational gradients. In: Proceedings of the seventh oak symposium: managing oak woodlands in a dynamic world. USDA Forest Service General Technical Report PSW-GTR-251, 433–445. [Abstract] [PDF]


Ortego J, Gugger PF, Riordan EC, Sork VL (2014) Influence of climatic niche suitability and geographic overlap on hybridization patterns among southern Californian oaks. Journal of Biogeography, 41(10):1895–1908, doi:10.1111/jbi.12334.

Gavin DG, Fitzpatrick M, Gugger PF, et al. (2014) Climate refugia: joint inference from fossil records, species distribution models, and phylogeography. New Phytologist, 204(1):37–54, doi:10.1111/nph.1292.


Gugger PF, Ikegami M, Sork VL (2013) Influence of late Quaternary climate change on present patterns of genetic variation in valley oak, Quercus lobata Née. Molecular Ecology, 22(13):3598–3612, doi:10.1111/mec.12317.

Gugger PF, Cavender-Bares J. (2013) Molecular and morphological support for a Florida origin of the Cuban oak. Journal of Biogeography, 40(4):632–645, doi:10.1111/j.1365-2699.2011.02610.x.


Ortego J, Riordan EC, Gugger PF, Sork VL (2012) Influence of environmental heterogeneity on genetic diversity and structure in an endemic southern Californian oak. Molecular Ecology, 21(13):3210–3223, doi:10.1111/j.1365-294X.2012.05591.x.


Gugger PF, González Rodríguez A, Rodríguez Correa H, Sugita S, Cavender-Bares J (2011) Southward Pleistocene migration of Douglas-fir into Mexico: phylogeography, ecological niche modeling, and conservation of ‘rear edge’ populations. New Phytologist, 189(4):1185–1199, doi:10.1111/j.1469-8137.2010.03559.x. [Commentary]


Gugger PF, Sugita S, Cavender-Bares J (2010) Phylogeography of Douglas-fir based on mitochondrial and chloroplast DNA sequences: testing hypotheses from the fossil record. Molecular Ecology, 19(9):1877–1897, doi:10.1111/j.1365-294X.2010.04622.x.

Gugger PF, Sugita S (2010) Glacial populations and postglacial migration of Douglas-fir based on fossil pollen and macrofossil evidence. Quaternary Science Reviews, 29(17-18):2052–2070, doi:10.1016/j.quascirev.2010.04.022.


Arnold AE, Miadlikowska J, Higgins KL, Sarvate SD, Gugger P, Way A, Hofstetter V, Kauff F, Lutzoni F (2009) A phylogenetic estimation of trophic transition networks for Ascomycetous fungi: are lichens cradles of symbiotrophic fungal diversification? Systematic Biology, 58(3):283–297, doi:10.1093/sysbio/syp001.


Gugger PF, McLachlan JS, Manos PS, Clark JS (2008) Inferring long-distance dispersal and topographic barriers during postglacial colonization from the genetic structure of red maple (Acer rubrum L.) in New England. Journal of Biogeography, 35(9):1665–1673, doi:10.1111/j.1365-2699.2008.01915.x.