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Author ORCID Identifier


Campus-Only Access for Five (5) Years

Document Type


Degree Name

Doctor of Philosophy (PhD)

Degree Program

Wildlife & Fisheries Conservation

Year Degree Awarded


Month Degree Awarded


First Advisor

Stephen DeStefano

Second Advisor

John Organ

Third Advisor

Warren Johnson

Fourth Advisor

Ms. Jennifer Vashon

Subject Categories

Genomics | Other Ecology and Evolutionary Biology | Population Biology | Zoology


Canada lynx (Lynx canadensis) are habitat- and prey-specialists associated with early successional boreal forests that support an abundance of their primary prey species, snowshoe hare (Lepus americanus). The species distribution dips into the northernmost United States, where lynx are listed as threatened under the US Endangered Species Act. Within the Northern Appalachian-Acadian ecoregion, habitat in Maine supports the largest and most robust population of lynx in the contiguous United States. However, suitable habitat is typically less abundant and more patchily distributed at the trailing edge of the species distribution, where peripheral populations are more at risk of isolation and associated impacts to resilience (e.g., genetic erosion). We developed a chromosome-scale reference genome for Canada lynx and used low-coverage whole genome sequences to better understand connectivity and gene flow between Maine and adjacent Canadian provinces. We detected genetic structure and resistance to gene flow shaped by isolating water bodies including the St. Lawrence River. Genome-wide diversity was lower at the trailing edge, which suggests populations at the range periphery may already be showing genetic impacts of isolation. Northward and upslope habitat contractions driven by climate change are expected to exacerbate isolation beyond 2050. Therefore, we used an ecological genomics approach to quantify the species’ capacity to evolve in response to changing conditions (i.e., adaptive potential). We identified gene-environment associations under current climate (1970-2000) and calculated the “genetic offset” required for lynx to retain those beneficial associations under future conditions (1961-1980). Our findings suggest that mismatch between current and future adaptive optima will require dramatic allelic turnover for some populations. However, adaptive potential at some functional loci is weakened by available standing variation, particularly among peripheral populations where genome-wide diversity is low. Further study is required to identify and conserve corridors which facilitate connectivity and gene flow between populations at the trailing edge and at the core of the species distribution. In 2018, the US Fish and Wildlife Service recommended Canada lynx for delisting from US Endangered Species Act protections. State and federal management agencies should consider incorporating a non-invasive genetic component to their post-delisting monitoring plans.