Canada lynx (Lynx canadensis) low-coverage whole genome resequencing

Anthropogenic climate change is on track to outpace habitat loss as the leading threat to biodiversity. Many species will rely upon range shifts, rapid evolution toward new behavioral and physiological optima, or both, to evade local extirpation and extinction. Range-shifts have been more broadly studied in the context of climate resiliency, but adaptive potential is rarely integrated into risk assessment and management planning. We used low-coverage whole genomes and current (1970-2000) and future (2061-2080) projected climate data to identify genetic variation associated with key climate variables across Maine and eastern Canadian provinces at the periphery of the Canada lynx (Lynx canadensis) distribution, where responses to a rapidly-changing environment should be most apparent. Canada lynx are cold-adapted mesocarnivores whose adaptations to hunting in deep, powdery snow provide a seasonal competitive advantage over generalist competitors including bobcat and coyote. However, projected warming of up to three degrees celsius by 2100 across lynx habitat in southeastern Canada and the northeastern United States will likely result in reduced snowfall. We identify putative climate-adaptive genetic variation among 61 lynx, explore functional pathways tied to environmental conditions and describe adaptive-mismatches between current and future conditions among three lynx populations. The Circadian Rhythm and Circadian Entrainment pathways were identified as highly enriched with climate-adaptive variation. However, genomic vulnerability estimates suggest that dramatic allelic shifts will be required to compensate for mismatches between current and future adaptive optima in these pathways. An assessment of allelic frequencies at loci within the Circadian Rhythm pathway indicates that limitations on standing variation could hamper necessary adaptive shifts. Our study reinforces the need to more broadly integrate adaptive potential into risk assessments, particularly for threatened and endangered species under Endangered Species Act protections.