Genomic Differentiation Along an Altitudinal–Longitudinal Gradient in Yarlung Zangbo Rock Agamas (Laudakia)

Extreme altitudinal gradients are natural experiments for testing how environmental gradients shape genomic variation, yet remain poorly characterised in high-altitude reptiles. We analysed whole-genome resequencing data (~17×) from 44 rock agamas (Laudakia sacra and L. wui) from five populations spanning 2311–3758 m in the Yarlung Zangbo valley, Qinghai–Tibet Plateau. Variation within L. sacra formed a continuous altitudinal cline rather than four discrete units, with the first principal component (PC1) explaining 41.29% of the variance; diversity declined monotonically with altitude (π fell ~9-fold), linkage disequilibrium (LD) half-decay lengthened 27-fold and the inbreeding coefficient (FROH) reached 0.155 with effective population size lowest at the valley head. Redundancy analysis with permutation identified 593 altitude-associated SNPs, jointly supported by a rank-based cline screen (6.1-fold enrichment over independence), and selective sweep analysis detected 4573 candidate genes across the ten pairwise comparisons, with the extreme interspecific contrast (C1 vs. C5) spanning cytoskeletal, epigenetic, glycolytic and oxygen-sensing functions. Low diversity, high inbreeding, small effective size and large projected genetic offset coincided at the valley head, making it the most genetically depauperate and climate-vulnerable population. These results reveal genomic differentiation along the altitudinal–longitudinal gradient consistent with putative incipient local adaptation and identify conservation priorities for high-altitude reptiles.