Hamilton Lab
Plant Evolutionary and Ecological Genetics

Research in the Hamilton lab broadly aims to understand the factors influencing the distribution of genetic variation across species' ranges in both natural and managed plant populations, focusing on those mechanisms that contribute to local adaptation.

We take an interdisciplinary approach to these challenges; combining population and landscape genomics with experimental quantitative and functional genomics. Our goal is to understand how genetic and environmental variation influence the expression of complex traits important to adaptation. Through this work we aim to increase our predictive power regarding the adaptive potential of populations for species management under climate change.

Current Research Interests

Genomic architecture of porous species boundaries: implications for climatic adaptation and hybrid breeding
(Funding: NSF-PGRP, Collaborators: Jason Holliday, Steve Keller & Matt Fitzpatrick) 
While high rates of intraspecific gene flow likely promote species cohesion, many tree species also show extensive interspecific hybridization where species overlap. This lack of reproductive isolation means that interspecific hybridization may be a source of evolutionary novelty outside the range of those found in the pure species. Combining genome-wide sequencing with phenotyping across large-scale provenance trials, this research aims to associate genomic ancestry with climatic gradients and adaptive phenotypes, predicting hybrid performance in a range of field test sites using Poplar, spruce and pine as model systems. This research leverages natural introgression zones to understand how interspecific genomic interactions yield desirable phenotypic outcomes across heterogeneous environments in a species of agronomic importance 

Trees in Peril: American Beech, Eastern Hemlock, and Three Eastern Ash Species. (Funding: TNC, Collaborators: USDA-Forest Service, University of Connecticut, University of Tennessee-Knoxville, University of Notre Dame, and many more)
In collaboration with several federal, state, NGO, and academic institutions our group is contributing to a region-wide restoration and breeding efforts for five of the most crucially threatened trees of the Eastern deciduous forest. Our group is focusing specifically on three ash species: Fraxinus pennsylvanica, F. americana and F. nigra leading species-specific ex situ seed  and leaf tissue collection coordination, range wide genomics assessment of populations to establish genotype-environment associations, and development of EAB-resistance breeding material through establishing species provenance trials. Broadly, the goal of this research will be to link genotype with phenotype across environments to inform breeding and restoration efforts related to the preservation of foundational ash species.

Genomics-driven monitoring of Oregon Ash for gene conservation and development of pre-breeding resources (Funding: USDA, Collaborators: Richard Sniezko, Wyatt Williams, Tim Thibault, Brian Dorsey, Jennifer Koch, and Tom Parchman)
The decimation of eastern hardwood forests in response to the Emerald Ash Borer emphasizes the imminent threat facing forest-based ecosystems and economies in the United States. To safeguard species at risk to EAB, conservation and restoration policies need genomic screening of seed and living collections to quantify genetic variation captured within and across conservation collections. This research establishes a genomic assessment of ex situ and living collections of Oregon Ash. We will create a genomic passport for Oregon ash maintained in collections for future use in genecology, seed orchard establishment, EAB-resistance breeding program development. These resources also provide a foundation for comparative work directly applicable to state and national forest health initiatives associated for ash species.

Genetic relatedness for naturally-regenerating American Chestnuts (Funding: The American Chestnut Foundation, Collaborators: Sara Fitzsimmons)
In collaboration with the American Chestnut Foundation, we are using naturally-regenerating populations of American Chestnut with known founders to evaluate genetic relatedness. The goal of this research is to understand and model the number and diversity of founders that may be needed for restoration plantings using American Chestnut. We are taking a genomics approach to evaluate relatedness and effective population size within populations that known founders and have known timing of population bottlenecks to model population outcomes following restoration scenarios. Our goal is to evaluate demographic and diversity metrics that will ensure the long-term evolutionary potential of restored American Chestnut populations.

​The evolution of barriers to reproduction in long-lived conifers: consequences for genetic rescue
​(Funding: NSF-RAPID, USFS, Morton Arboretum, Collaborators: Jessica Wright, Tom Parchman, Sean Hoban)
Weak barriers to reproduction, but often-observed asymmetries, impact species determination and management. We are combining the use of an experimental common garden with multiple generations (parent, F1, and F2) with genome scans to provide fundamental insights into the evolution of reproductive barriers in conifers using Torrey pine (Pinus torreyana Parry), one of the rarest pine species in the world. This research considers the long-term impact of genetic rescue in the conservation of rare species and will assess the fine-scale distribution of genetic variation and relatedness among individuals in the natural populations to inform conservation management priorities. 

The importance of adaptation in restoration: conservation of the adaptive state and process for climate-resilient grasslands
​(Funding: TNC, Collaborators: Marissa Ahlering)
One of the major challenges to restoration is identifying seeds to source for restoration, particularly as restoration success will be influenced by adaptation to the restoration environment. This research aims to empirically test models evaluating the role environmental heterogeneity and migration have on the evolution of plasticity or genetic differences across a species' range. Currently, my research program uses a combination of quantitative genetic tools, population genetic tools, and climate modeling to understand the scale of local adaptation important to successful restoration of prairie ecosystems, focusing on non-crop Asteraceae and Rosaceae. 

Evolutionary change during restoration: genomic consequences of propagation in seed sourced for restoration
​(Funding: USDA, Collaborators: Jarrad Prasifka)
Agricultural propagation of native seed material for restoration can lead to evolutionary change, however cultivation of wild seed may be necessary to keep pace with restoration needs. We are currently evaluating the impact propagation has had on genomic diversity between ex situ, native and commercial seed collections. In the future, we will complement this with further genomic and phenotypic comparisons between seed sources to test for evolutionary change over time (native v. ex situ) and in response to cultivation (native vs. commercial). 

The role of genome duplication in niche divergence and colonization
(Funding: NDSU, Collaborators: Mike Barker & Katrina Dlugosch)
Following WGD, there is good evidence that polyploids diverge ecologically from their diploid progenitors, exhibiting an increased rate of niche evolution relative to diploids. However, a major outstanding question in evolutionary biology asks how ploidy-level changes contribute to niche evolution. We are examining the consequences of ploidy-level changes to niche divergence in Geum triflorum, a perennial allohexaploid that spans a range of distinct environments, focusing on the evolution and expression of genetic variation across duplicate genes associated with different ancestral sub-genomes. 

Creating a predictive framework for cold tolerance in North Dakota grape cultivars
(Funding: USDA, Collaborators: Harlene Hatterman-Valenti, Red Trail Vineyard)
Response to environmental cues varies widely across grape cultivars with large impacts to both yield and vineyard sustainability. This project aims to comprehensively assess the interaction between temperature cues, phenology, and cold hardiness across multiple growing seasons in grape cultivars. This project will systematically assess the fine-scale relationship between temperature and the induction and breakup of dormancy and dormancy-related traits.




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