Abstract: Understanding the genetic diversity and genetic load of endangered species is essential for developing effective conservation strategies, particularly in ecologically sensitive regions such as the Himalayas. Cupressus austrotibetica, a rare conifer and the tallest recorded tree in Asia, reaching up to 101.2 m, faces substantial anthropogenic and environmental threats. To evaluate its genetic status, we sequenced transcriptomes of 54 individuals sampled across its restricted range and compared them with 96 individuals of C. gigantea, a closely related endangered species with broader distribution at higher elevations. Our analysis reveals that C. austrotibetica exhibits higher genetic diversity (π = 0.0091) compared to C. gigantea (π = 0.0042). Demographic analyses identified three historical bottleneck events in C. austrotibetica and two in C. gigantea, with two of these events coinciding with Quaternary climatic oscillations. Despite its relatively high genetic diversity, C. austrotibetica has a smaller effective population size based on Stairway Plot 2 (Nₑ ≈ 7200) than C. gigantea (Nₑ ≈ 17 600). Furthermore, C. austrotibetica harbors a higher proportion of severe deleterious mutations, while C. gigantea retains more moderate deleterious variants. These findings indicate that a recent anthropogenic bottleneck event has likely driven the reduced population size and increased genetic load in C. austrotibetica, emphasizing the urgent need for conservation priorities for this imperiled species.

Key words: Conservation, genetic diversity, genetic load, rare cypress, small population