Hamilton Lab
Plant Evolutionary and Ecological Genetics
Published manuscripts (*undergraduate, **graduate, ***postdoctoral researcher)
Mead, A.***, Beasley-Bennett, J. R., Bleich, A., Fischer, D., Flint, S., Golightly, J., Klopf, S. K., Kulbaba, M.W., Lasky, J. R., LeBoldus, J. M., Lowry, D. B., Mitchell, N., Moran, E., Sexton, J. P., Sondreli, K. L., Worthing, B., Zavala-Paez, M.**, Fitzpatrick, M.C., Holliday, J., Keller, S., and J.A. Hamilton (Submitted) Variation in responses to temperature across admixed genotypes of Populus trichocarpa x P. balsamifera predict geographic shifts in regions where hybrids are favored
Zavala-Paez, M.**, Sutara, B.,* Keller, S., Holliday, J., Fitzpatrick, M., and J.A. Hamilton (Submitted) The role of cytonuclear interactions to plant adaptation across a Populus hybrid zone (Available on BioRxiv)
Hamilton, J.A. (Submitted) Molecular passports for ex situ collections: enhanced genetic monitoring for conservation.
Di Santo, L.**, Mead, A.***, Wright, J. and J.A. Hamilton (2025) Genetic basis of reproductive isolation in Torrey Pine (Pinus torreyana Parry): insights from hybridization and adaptation. Evolutionary Applications 18: e70094.
Rana, S.K.***, Lindstrom, J.**, Lehrer, M.A.***, Ahlering, M., and J.A. Hamilton (2025) Forecasting hotspots of grassland suitability under climate change for restoration. Biological Conservation 302: 110988 *Special Issue: Addressing complex drivers of land degradation via adaptive management*
McLaughlin, C. M., Hinshaw, C., Sandoval-Arango, S., Zavala-Paez, M.**, and J.A. Hamilton (2025) Redlisting genetics: towards inclusion of genetic data in IUCN Red List assessments. Conservation Genetics
Melton, A.E.***, Faske, T. M., Sniezko, R., Thibault, T., Williams, W., Parchman, T. L., and J.A. Hamilton (2025) Genomics-driven monitoring of Oregon ash (Fraxinus latifolia) to inform conservation and EAB-resistance breeding. Molecular Ecology *Special Issue on Conservation Genomics - Making a Difference*
Bolte, C.E.***, Phannareth, T., Zavala-Paez, M.**, Sutara, B.*, Fitzpatrick, M., Holliday, J., Keller, S., and J.A. Hamilton (2024) Genomic insights into hybrid zone formation: the role of climate, landscape, and demography in the emergence of a novel hybrid lineage. Molecular Ecology. 33: e17430
Sullivan, L. L., Portlas, Z. M.*, Jaeger, K., Hoffner, M.*, and J. A. Hamilton (2024) Climate and habitat type interact to influence contemporary dispersal potential in Prairie Smoke (Geum triflorum). Ecology and Evolution. 14: e11231
Zavala-Paez, M**, Holliday, J., and J.A. Hamilton (2024) Leveraging whole genome sequencing to estimate telomere length in plants. Molecular Ecology Resources. 2: e13899
Lindstrom, J.**, Ahlering, M, and J.A. Hamilton (2023) Seed sourcing for climate-resilient grasslands: the role of seed source diversity during early restoration establishment. Ecology and Evolution. 13: e10756
Lehrer, M.A.*** and J.A. Hamilton (2023) Preserving range-wide genetic diversity of Fraxinus nigra. Tree Seed Working Group News Bulletin, Canadian Forest Genetics Association 74: 17-21.
Kulbaba, M., Yoko, Z.**, and J.A. Hamilton (2023) Chasing the fitness optimum: temporal variation in the genetic and environmental expression of life-history traits for a perennial plant. Annals of Botany 7: 1191-1204
* Featured Perspective by Meredith Zettlemoyer
Keagy, J., Drummond, C., Gilbert, K., Grozinger, C., Hamilton, J., Hines, H., Lasky, J., Logan, C., Sawers, R., and T. Wagner (2023) Landscape transcriptomics as a tool for addressing global change effects across diverse species. Molecular Ecology Resources
Volk, K.**, Braasch, J.***, Ahlering, M., and J.A. Hamilton (2022) Environmental contributions to the evolution of trait differences in Geum triflorum: implications for restoration. American Journal of Botany *Special Issue on 'Approaches to the study of quantitative fitness-related traits'
Di Santo, L.N.**, Hoban, S.M., Parchman, T.L., Wright, J.W., and J.A. Hamilton (2022) Reduced representation sequencing to understand the evolutionary history of Torrey pine (Pinus torreyana) with implications for rare species conservation. Molecular Ecology 31: 4622-4639.
Benomar, L., Elferjani, R., Hamilton, J.A., O'Neill, G. A., Echchakoui, S., Bergeron, Y., and L. Mebarek (2022) Bibliometric analysis of the structure and evolution of research on assisted migration. Current Forestry Reports
VanWallendael, A., Lowry, D.B., and J.A. Hamilton (2022) One hundred years into the study of ecotypes, new advances are being made through large-scale field experiments in perennial plant systems. Current Opinion in Plant Biology. 66: 102152
Galla, S., Brown, L., Couch-Lewis, Y., Cubrinovska, I., Eason, D., Gooley, R., Hamilton, J.A., Heath, J., Hauser, S., Latch, E., Matocq, M., Richardson, A., Wold, J., Hogg, C., Santure, A., and T. Steeves (2022) The relevance of pedigrees in the conservation genomics era. Molecular Ecology 31: 41-54.
Di Santo, L.N.**, Polgar, M.*, Nies, S.*, Hodgkiss, P., Canning, C.A., Wright, J.W. and J.A. Hamilton (2021) Seed morphology and emergence variability in a conservation collection of Pinus torreyana. AOB Plants. 13 (5): plab058.
Braasch, J.E.***, Di Santo, L.N.**, Tarble, Z.*, Prasifka, J.R., and J.A. Hamilton (2021) Testing for evolutionary change in restoration: a genomic comparison between ex situ, native and commercial seed sources of Helianthus maximiliani. Evolutionary Applications. 14: 2206-2220.
Di Santo, L, N.** and J. A. Hamilton (2021) Environmental and geographic data optimize ex situ collections and the preservation of adaptive evolutionary potential. Conservation Biology 35: 733-744.
Yoko, Z.**, Volk, K.*, Dochtermann, N., and J. A. Hamilton (2020) The importance of quantitative trait differentiation in restoration: landscape heterogeneity and functional traits inform seed transfer guidelines. AOB Plants. **Special Issue on The Ecology and Genetics of Population Differentiation in Plants**
Hamilton, J.A., Flint, S., Lindstrom, J.**, Volk, K.**, Shaw, R., and M. Aherling (2020) Evolutionary approaches to seed sourcing for grassland restorations. New Phytologist 225: 2246-2248.
Martinez-Berdeja, A., Hamilton, J.A., Bontemps, A., Schmitt, J., and J.W. Wright (2019) Evidence for population differentiation among Jeffrey and Ponderosa pines in survival, growth and phenology. Forest Ecology and Management. 434: 40-48.
Hamilton, J.A. and Z. Tarble* (2018) Developing quantitative skills for ecological data: the effects of climate warming on phenological variation and species interactions. Dig Into Data FMN. QUBES Educational Resources. doi:10.25334/Q44Q7G
Hamilton, J.A., and J. M. Miller (2018) From transects to transcripts: teasing apart the architecture of reproductive barriers. Molecular Ecology. 27: 1339-1341.
Hamilton, J. A., Royauté , R., Wright, J. W., Hodgskiss, P., and F. T. Ledig (2017) Genetic conservation and management of the California endemic, Torrey pine (Pinus torreyana Parry): implications of genetic rescue in a genetically depauperate species. Ecology & Evolution 7(18): 7370-7381.
Janes, J. K. and J.A. Hamilton (2017) Mixing it up: the role of hybridization in forest management and conservation under climate change. Forests 8 (7): 237 **Special Issue on New Insights into Climate Sensitivity of Forest Growth, Health, and Disturbance: Vulnerability, Resilience, and Change**
Hamilton, J.A., El Kayal, W., Hart, A., Runcie, D.E., , Arango-Velez, A. and J. Cooke (2016) The joint influence of photoperiod and temperature during growth cessation and development of dormancy in white spruce (Picea glauca). Tree Physiology 36 (11): 1432-1448.
Hamilton, J.A. and J. M. Miller (2016) Adaptive introgression as a resource for management and genetic conservation under climate change. Conservation Biology 30 (1): 33-41.
*Featured in the Molecular Ecologist (July 8, 2015)
*Featured in WILDLIFESNPITS (July 10, 2015)
*Featured in the Molecular Ecology (November 2, 2015)
Miller, J. M., and J.A. Hamilton. (2016) Interspecies hybridization merits consideration in the conservation toolbox: response to Kovach et al. 2016. Conservation Biology 30 (2): 431-433.
Cullingham, C.I., Thiessen, C., Derocher, A. Pacquet, P., Miller, J., Hamilton, J.A. and D. W. Coltman (2016) Population structure and dispersal of wolves in the Canadian Rocky Mountains. Journal of Mammalogy 97 (3): 839-851.
Hamilton, J.A., Okado, M., Korves, T. and J. Schmitt (2015) The role of climate adaptation in colonization success in Arabidopsis thaliana. Molecular Ecology 9: 2253-2263. **Special Issue on Invasion Genetics: the Baker and Stebbins Legacy**
Hamilton, J.A., De La Torre, A.R., and S.N. Aitken (2015) Fine-scale environmental variation contributes to introgression in a three-species spruce hybrid complex. Tree Genetics and Genomes 11:1-4
Hamilton, J.A. and S.N. Aitken (2013) Genetics and morphology of a spruce (Picea sitchensis x P. glauca) hybrid zones along a precipitation gradient. American Journal of Botany 100:1651-1662bsapubs.onlinelibrary.wiley.com/doi/full/10.3732/ajb.1200654
Hamilton, J.A., Lexer, C., and S.N. Aitken (2013) Genomic and phenotypic architecture of a spruce hybrid zone (Picea sitchensis x P. glauca). Molecular Ecology 22:827-841. **Special Issue on Evolutionary Ecological Genomics**
Hamilton, J.A., Lexer, C. and S.N. Aitken (2013) Differential introgression reveals candidates for selection across a spruce (Picea sitchensis x P. glauca) hybrid zones. New Phytologist 197: 927-938
Gornish, E.S., Hamilton, J.A., Barberan, A., Benito, B.M., Binzer, A., DeMeester, J.E., Gruwez, R., Moreira, B., Taheri, S., Tomiolo, S., Vinagre, C., Vuarin, P. and J. Weaver (2013) Interdisciplinary climate change collaborations are essential for early-career scientists. EOS: Transactions of the American Geophysical Union 94(16):151
Hamilton, J.A. and C.G. Eckert (2007) Population genetic consequences of geographic disjunction: a prairie plant species isolated on Great Lakes alvars. Molecular Ecology 16: 1649-1660
Book chapters:
Hamilton, J.A., Okada, M., Korves, T. and J. Schmitt (2016) The role of climate adaptation in colonization success in Arabidopsis thaliana. In Barrett, S.C.H., Colautti, R.I., Dlugosch, K. M., and L. H. Rieseberg, editors. Invasion Genetics: The Baker and Stebbins Legacy, Wiley-Blackwell, West Sussex, UK.
Stockwell, C.A., Kinnison, M.T., Hendry, A.P. and J.A. Hamilton (2016) Evolutionary Restoration Ecology. In Falk, D.A., Palmer, M.A., and J.B. Zedler, editors. Foundations of Restoration Ecology. Island Press, Washington.
Mead, A.***, Beasley-Bennett, J. R., Bleich, A., Fischer, D., Flint, S., Golightly, J., Klopf, S. K., Kulbaba, M.W., Lasky, J. R., LeBoldus, J. M., Lowry, D. B., Mitchell, N., Moran, E., Sexton, J. P., Sondreli, K. L., Worthing, B., Zavala-Paez, M.**, Fitzpatrick, M.C., Holliday, J., Keller, S., and J.A. Hamilton (Submitted) Variation in responses to temperature across admixed genotypes of Populus trichocarpa x P. balsamifera predict geographic shifts in regions where hybrids are favored
Zavala-Paez, M.**, Sutara, B.,* Keller, S., Holliday, J., Fitzpatrick, M., and J.A. Hamilton (Submitted) The role of cytonuclear interactions to plant adaptation across a Populus hybrid zone (Available on BioRxiv)
Hamilton, J.A. (Submitted) Molecular passports for ex situ collections: enhanced genetic monitoring for conservation.
Di Santo, L.**, Mead, A.***, Wright, J. and J.A. Hamilton (2025) Genetic basis of reproductive isolation in Torrey Pine (Pinus torreyana Parry): insights from hybridization and adaptation. Evolutionary Applications 18: e70094.
Rana, S.K.***, Lindstrom, J.**, Lehrer, M.A.***, Ahlering, M., and J.A. Hamilton (2025) Forecasting hotspots of grassland suitability under climate change for restoration. Biological Conservation 302: 110988 *Special Issue: Addressing complex drivers of land degradation via adaptive management*
McLaughlin, C. M., Hinshaw, C., Sandoval-Arango, S., Zavala-Paez, M.**, and J.A. Hamilton (2025) Redlisting genetics: towards inclusion of genetic data in IUCN Red List assessments. Conservation Genetics
Melton, A.E.***, Faske, T. M., Sniezko, R., Thibault, T., Williams, W., Parchman, T. L., and J.A. Hamilton (2025) Genomics-driven monitoring of Oregon ash (Fraxinus latifolia) to inform conservation and EAB-resistance breeding. Molecular Ecology *Special Issue on Conservation Genomics - Making a Difference*
Bolte, C.E.***, Phannareth, T., Zavala-Paez, M.**, Sutara, B.*, Fitzpatrick, M., Holliday, J., Keller, S., and J.A. Hamilton (2024) Genomic insights into hybrid zone formation: the role of climate, landscape, and demography in the emergence of a novel hybrid lineage. Molecular Ecology. 33: e17430
Sullivan, L. L., Portlas, Z. M.*, Jaeger, K., Hoffner, M.*, and J. A. Hamilton (2024) Climate and habitat type interact to influence contemporary dispersal potential in Prairie Smoke (Geum triflorum). Ecology and Evolution. 14: e11231
Zavala-Paez, M**, Holliday, J., and J.A. Hamilton (2024) Leveraging whole genome sequencing to estimate telomere length in plants. Molecular Ecology Resources. 2: e13899
Lindstrom, J.**, Ahlering, M, and J.A. Hamilton (2023) Seed sourcing for climate-resilient grasslands: the role of seed source diversity during early restoration establishment. Ecology and Evolution. 13: e10756
Lehrer, M.A.*** and J.A. Hamilton (2023) Preserving range-wide genetic diversity of Fraxinus nigra. Tree Seed Working Group News Bulletin, Canadian Forest Genetics Association 74: 17-21.
Kulbaba, M., Yoko, Z.**, and J.A. Hamilton (2023) Chasing the fitness optimum: temporal variation in the genetic and environmental expression of life-history traits for a perennial plant. Annals of Botany 7: 1191-1204
* Featured Perspective by Meredith Zettlemoyer
Keagy, J., Drummond, C., Gilbert, K., Grozinger, C., Hamilton, J., Hines, H., Lasky, J., Logan, C., Sawers, R., and T. Wagner (2023) Landscape transcriptomics as a tool for addressing global change effects across diverse species. Molecular Ecology Resources
Volk, K.**, Braasch, J.***, Ahlering, M., and J.A. Hamilton (2022) Environmental contributions to the evolution of trait differences in Geum triflorum: implications for restoration. American Journal of Botany *Special Issue on 'Approaches to the study of quantitative fitness-related traits'
Di Santo, L.N.**, Hoban, S.M., Parchman, T.L., Wright, J.W., and J.A. Hamilton (2022) Reduced representation sequencing to understand the evolutionary history of Torrey pine (Pinus torreyana) with implications for rare species conservation. Molecular Ecology 31: 4622-4639.
Benomar, L., Elferjani, R., Hamilton, J.A., O'Neill, G. A., Echchakoui, S., Bergeron, Y., and L. Mebarek (2022) Bibliometric analysis of the structure and evolution of research on assisted migration. Current Forestry Reports
VanWallendael, A., Lowry, D.B., and J.A. Hamilton (2022) One hundred years into the study of ecotypes, new advances are being made through large-scale field experiments in perennial plant systems. Current Opinion in Plant Biology. 66: 102152
Galla, S., Brown, L., Couch-Lewis, Y., Cubrinovska, I., Eason, D., Gooley, R., Hamilton, J.A., Heath, J., Hauser, S., Latch, E., Matocq, M., Richardson, A., Wold, J., Hogg, C., Santure, A., and T. Steeves (2022) The relevance of pedigrees in the conservation genomics era. Molecular Ecology 31: 41-54.
Di Santo, L.N.**, Polgar, M.*, Nies, S.*, Hodgkiss, P., Canning, C.A., Wright, J.W. and J.A. Hamilton (2021) Seed morphology and emergence variability in a conservation collection of Pinus torreyana. AOB Plants. 13 (5): plab058.
Braasch, J.E.***, Di Santo, L.N.**, Tarble, Z.*, Prasifka, J.R., and J.A. Hamilton (2021) Testing for evolutionary change in restoration: a genomic comparison between ex situ, native and commercial seed sources of Helianthus maximiliani. Evolutionary Applications. 14: 2206-2220.
Di Santo, L, N.** and J. A. Hamilton (2021) Environmental and geographic data optimize ex situ collections and the preservation of adaptive evolutionary potential. Conservation Biology 35: 733-744.
Yoko, Z.**, Volk, K.*, Dochtermann, N., and J. A. Hamilton (2020) The importance of quantitative trait differentiation in restoration: landscape heterogeneity and functional traits inform seed transfer guidelines. AOB Plants. **Special Issue on The Ecology and Genetics of Population Differentiation in Plants**
Hamilton, J.A., Flint, S., Lindstrom, J.**, Volk, K.**, Shaw, R., and M. Aherling (2020) Evolutionary approaches to seed sourcing for grassland restorations. New Phytologist 225: 2246-2248.
Martinez-Berdeja, A., Hamilton, J.A., Bontemps, A., Schmitt, J., and J.W. Wright (2019) Evidence for population differentiation among Jeffrey and Ponderosa pines in survival, growth and phenology. Forest Ecology and Management. 434: 40-48.
Hamilton, J.A. and Z. Tarble* (2018) Developing quantitative skills for ecological data: the effects of climate warming on phenological variation and species interactions. Dig Into Data FMN. QUBES Educational Resources. doi:10.25334/Q44Q7G
Hamilton, J.A., and J. M. Miller (2018) From transects to transcripts: teasing apart the architecture of reproductive barriers. Molecular Ecology. 27: 1339-1341.
Hamilton, J. A., Royauté , R., Wright, J. W., Hodgskiss, P., and F. T. Ledig (2017) Genetic conservation and management of the California endemic, Torrey pine (Pinus torreyana Parry): implications of genetic rescue in a genetically depauperate species. Ecology & Evolution 7(18): 7370-7381.
Janes, J. K. and J.A. Hamilton (2017) Mixing it up: the role of hybridization in forest management and conservation under climate change. Forests 8 (7): 237 **Special Issue on New Insights into Climate Sensitivity of Forest Growth, Health, and Disturbance: Vulnerability, Resilience, and Change**
Hamilton, J.A., El Kayal, W., Hart, A., Runcie, D.E., , Arango-Velez, A. and J. Cooke (2016) The joint influence of photoperiod and temperature during growth cessation and development of dormancy in white spruce (Picea glauca). Tree Physiology 36 (11): 1432-1448.
Hamilton, J.A. and J. M. Miller (2016) Adaptive introgression as a resource for management and genetic conservation under climate change. Conservation Biology 30 (1): 33-41.
*Featured in the Molecular Ecologist (July 8, 2015)
*Featured in WILDLIFESNPITS (July 10, 2015)
*Featured in the Molecular Ecology (November 2, 2015)
Miller, J. M., and J.A. Hamilton. (2016) Interspecies hybridization merits consideration in the conservation toolbox: response to Kovach et al. 2016. Conservation Biology 30 (2): 431-433.
Cullingham, C.I., Thiessen, C., Derocher, A. Pacquet, P., Miller, J., Hamilton, J.A. and D. W. Coltman (2016) Population structure and dispersal of wolves in the Canadian Rocky Mountains. Journal of Mammalogy 97 (3): 839-851.
Hamilton, J.A., Okado, M., Korves, T. and J. Schmitt (2015) The role of climate adaptation in colonization success in Arabidopsis thaliana. Molecular Ecology 9: 2253-2263. **Special Issue on Invasion Genetics: the Baker and Stebbins Legacy**
Hamilton, J.A., De La Torre, A.R., and S.N. Aitken (2015) Fine-scale environmental variation contributes to introgression in a three-species spruce hybrid complex. Tree Genetics and Genomes 11:1-4
Hamilton, J.A. and S.N. Aitken (2013) Genetics and morphology of a spruce (Picea sitchensis x P. glauca) hybrid zones along a precipitation gradient. American Journal of Botany 100:1651-1662bsapubs.onlinelibrary.wiley.com/doi/full/10.3732/ajb.1200654
Hamilton, J.A., Lexer, C., and S.N. Aitken (2013) Genomic and phenotypic architecture of a spruce hybrid zone (Picea sitchensis x P. glauca). Molecular Ecology 22:827-841. **Special Issue on Evolutionary Ecological Genomics**
Hamilton, J.A., Lexer, C. and S.N. Aitken (2013) Differential introgression reveals candidates for selection across a spruce (Picea sitchensis x P. glauca) hybrid zones. New Phytologist 197: 927-938
Gornish, E.S., Hamilton, J.A., Barberan, A., Benito, B.M., Binzer, A., DeMeester, J.E., Gruwez, R., Moreira, B., Taheri, S., Tomiolo, S., Vinagre, C., Vuarin, P. and J. Weaver (2013) Interdisciplinary climate change collaborations are essential for early-career scientists. EOS: Transactions of the American Geophysical Union 94(16):151
Hamilton, J.A. and C.G. Eckert (2007) Population genetic consequences of geographic disjunction: a prairie plant species isolated on Great Lakes alvars. Molecular Ecology 16: 1649-1660
Book chapters:
Hamilton, J.A., Okada, M., Korves, T. and J. Schmitt (2016) The role of climate adaptation in colonization success in Arabidopsis thaliana. In Barrett, S.C.H., Colautti, R.I., Dlugosch, K. M., and L. H. Rieseberg, editors. Invasion Genetics: The Baker and Stebbins Legacy, Wiley-Blackwell, West Sussex, UK.
Stockwell, C.A., Kinnison, M.T., Hendry, A.P. and J.A. Hamilton (2016) Evolutionary Restoration Ecology. In Falk, D.A., Palmer, M.A., and J.B. Zedler, editors. Foundations of Restoration Ecology. Island Press, Washington.