Genomic Diversity of the Endangered Guinan Toad‐Headed Lizard and Its Conservation Implications

ABSTRACT The Guinan toad‐headed lizard, Phrynocephalus guinanensis , is a small reptilian species restricted only to the Mugetan Desert on the northeastern corner of the Qinghai–Xizang Plateau. This species faces endangerment due to its extremely narrow distribution range, combined with progressively increasing human activities recently. However, a conservation genomic assessment of P. guinanensis remains uninvestigated, thus resulting in a limited understanding of the genetic diversity of this species. Here, we assembled a high‐quality reference genome for P. guinanensis using HiFi sequencing technology and conducted a comprehensive assessment of its population genetic diversity by integrating data from 191 individuals across 14 populations. The updated genome size was 1.84 Gb with a scaffold N50 of 133.2 Mb, and 21 884 coding genes were annotated. The lower genetic diversity (mean π = 1.0253 × 10 −3 , mean heterozygosity = 8.8150 × 10 −4 ), higher inbreeding levels (mean F ROH = 0.0778), and an elevated mutation load (mean Missense = 0.5660, mean LOF = 0.5689) were detected in P. guinanensis . Based on the demographic simulation, this species has experienced a significant decrease in effective population size. Our results indicated that P. guinanensis is undergoing severe genetic erosion, which may compromise its adaptive potential and increase its extinction risk. We therefore propose prioritizing genetically diverse populations as a source for captive breeding and long‐term field monitoring to ensure the viability of P. guinanensis . Our study enriches the understanding of the Guinan toad‐headed lizard's genetic diversity, providing useful genomic resources for conservation strategies on this species.