Seasonal Dietary Patterns of Tarim Red Deer (Cervus hanglu yarkandensis) Revealed by the trnL Sequencing Approach in the Tarim River Basin (Xinjiang, China)

The Tarim red deer (Cervus hanglu yarkandensis) is a flagship species inhabiting the Euphrates poplar (Populus euphratica) riparian forests along the Tarim River in China. It is listed as a Class I nationally protected species but despite its importance, current knowledge about this subspecies remains limited, particularly regarding the seasonal variation in its foraging ecology within the Shaya region of Xinjiang—a landscape characterized by a mosaic of Euphrates poplar forests interspersed with cotton (Gossypium hirsutum) croplands. We used DNA metabarcoding technology to investigate the diet of the Tarim red deer during the summer and winter of 2021–2022. We targeted chloroplast gene trnL (c–h) region for plant identification. From a total of 39 fecal samples analyzed, we identified 50 plant species; based on the frequency of occurrence, the primary food items of Tarim red deer were cotton (38.75%) and Euphrates poplar (36.87%). Other species were consumed occasionally, including common reed (Phragmites australis, 7.00%), common salt tree (Halimodendron halodendron, 6.13%), goosefoot (Chenopodium album, 4.67%), licorice (Glycyrrhiza inflata, 3.50%), slender branch saltwort (Kalidium gracile, 0.28%), Chinese licorice (Glycyrrhiza glabra, 0.25%), elegant false tamarisk (Myrtama elegans, 0.16%), and Oriental dodartia (Dodartia orientalis, 0.07%). As expected, both the Shannon diversity index and species richness were significantly higher in summer than in winter (p < 0.05), whereas the dietary niche breadth was significantly lower in winter (p < 0.05). Overall, our results indicate that the Tarim red deer is a seasonally adaptable mixed feeder. This study provides valuable insights into the foraging ecology of this endangered subspecies and offers scientific evidence to support its management and conservation. In particular, we stress the importance of cotton in their diet and stressed that measures of mitigation could affect the conservation of this endangered population.