Comparative Analysis of the Mitochondrial Genome and Population Evolution in the Chinese Giant Salamander (Andrias davidianus)

Mitochondrial genomes provide powerful insights into evolutionary history, population structure, and conservation genetics. Here, we analyzed complete mitochondrial genomes (mitogenomes) from 38 Chinese giant salamanders (Andrias davidianus, CGSs) sampled from both wild and conservation-bred populations. CGS mitogenomes exhibited remarkable structural conservation, yet pronounced heterogeneity in nucleotide diversity, selection regimes, and repetitive element distributions across lineages. Cytb and ND3 showed elevated intraspecific variability relative to the standard cox1 barcode, highlighting their superior resolution for fine-scale population analyses. Although most mitochondrial genes were subject to strong purifying selection, lineage-specific signals of positive selection were detected in ND2, and a rare, potentially deleterious frameshift mutation was identified in ND1 from a captive individual. Lineage-associated variation in mitogenomic SSRs and widespread mito-nuclear phylogenetic discordance revealed a highly admixed population structure shaped by historical connectivity and introgression. Together, our results underscore the value of integrative mitogenomic analyses for resolving complex evolutionary histories and informing conservation management of endangered amphibians.