Mitochondrial genomic variations shed light on the phylogeny and biogeography of the Phrynocephalus guttatus species group (Reptilia: Agamidae) in arid Central Asia

The lizard genus Phrynocephalus is an emerging model for studying mitochondrial genome evolution. Within this genus, the P. guttatus species-group represents a taxonomically and ecologically diverse clade whose evolutionary relationships remain poorly resolved. Previous studies based on morphology and partial molecular data have been unable to fully clarify relationships within this rapidly radiated group. Complete mitochondrial genomes provide a solid basement to clarify phylogenetic relationships and assess the role of genomic structural variation in diversification. We sequenced and assembled the complete mitochondrial genomes from multiple representatives of the P. guttatus complex across Central Asia and performed comprehensive analyses including annotation, phylogenetic reconstruction, molecular dating, and biogeography assessment. Mitogenomic data resolved phylogenetic relationships with strong support and revealed pronounced structural dynamism, including lineage-specific tRNA duplications and rearrangements. Eastern lineages (P. melanurus 1 and 2, P. kuschakewitschii) differed from western taxa (P. g. kalmykus, P. g. guttatus) in tRNA composition, control region numbers, and rearrangement patterns. Eastern species exhibited duplication of tRNA-Phe and up to three control regions. Novel rearrangement types (F-, G-, and H-types) expand existing mitogenomic classification schemes. Divergence time analyses placed the initial radiation in the Late Miocene ‒ Pliocene (~ 3.13 Mya), with a major eastern diversification between 2.72 and 0.31 Mya, correlating with intense aridification of Central Asia. Ancestral range reconstruction indicated an origin in the Dzungar Basin, followed by dispersal and vicariance events driven by climatic and orographic changes. Our study establishes a robust mitogenome-based phylogenetic framework for the P. guttatus complex and demonstrates that its diversification was shaped by Neogene environmental dynamics and intrinsic mitochondrial genome rearrangements. The discovery of lineage-specific structural changes highlight the evolutionary significance plasticity in desert lizards adaptation.