Sex- and age-dependent physiological adaptation of captive père david’s deer revealed by multi-omics analysis

Understanding how age and sex influence molecular and physiological changes is essential for studying endangered species, particularly Père David’s deer, which is extinct in the wild. In this study, multi-omics analyses were performed to investigate transcriptomic, metabolomic, and proteomic dynamics in male and female Père David’s deer across different developmental stages under captive conditions. The results revealed sex- and stage-specific molecular trajectories, with males showing enhanced ion metabolism during early life and females exhibiting increased lipid metabolism during the subadult stage. A substantial proportion of differentially abundant metabolites and differentially expressed proteins were associated with immune and inflammatory processes. Transcriptome-based age estimation indicated that individuals at the Fawn stage exhibited younger transcriptomic profiles, and enrichment analysis of highly weighted genes highlighted immune-related pathways. In addition, transcriptomic deconvolution analysis revealed coordinated alterations in innate and adaptive immune cell populations during development. These findings provide a comprehensive multi-omics characterization of molecular and immune dynamics in captive Père David’s deer and improve understanding of developmental and sex-associated biological variation in this endangered species.