Abstract
Cupressaceae is a conifer family rich in plants of horticultural importance, including Cupressus, Chamaecyparis, Juniperus, and Thuja, yet genomic surveys are lacking for this family. Cupressus gigantea, one of the many rare conifers that are threatened by climate change and anthropogenic habitat fragmentation, plays an ever-increasing role in ecotourism in Tibet. To infer how past climate change has shaped the population evolution of this species, we generated a de novo chromosome-scale genome (10.92 Gb) and compared the species' population history and genetic load with that of a widespread close relative, C. duclouxiana. Our demographic analyses, based on 83 re-sequenced individuals from multiple populations of the two species, revealed a sharp decline of population sizes during the first part of the Quaternary. However, populations of C. duclouxiana then started to recover, while C. gigantea populations continued to decrease until recently. The total genomic diversity of C. gigantea is smaller than that of C. duclouxiana, but contrary to expectations, C. gigantea has fewer highly and mildly deleterious mutations than C. duclouxiana, and simulations and statistical tests support purifying selection during prolonged inbreeding as the explanation. Our results highlight the evolutionary consequences of decreased population size on the genetic burden of a long-lived endangered conifer with large genome size and suggest that genetic purging deserves more attention in conservation management.