Next-Generation Sequencing of Fecal DNA: A Novel Insight Into the Mitogenome Phylogeography of the Snow Leopard (Panthera Uncia)

Fecal samples are commonly used in conservation genetics for endangered and elusive species such as the snow leopard (Panthera uncia). However, the limited quantity and low quality of endogenous DNA in these samples present a challenge for acquiring genetic and genomic data. Previous studies of snow leopard mitochondrial DNA (mtDNA) phylogeography have produced inconsistent results, likely due to the limited sequencing length of PCR-based methods. To address this limitation, we performed Next-Generation Sequencing (NGS) on 19 fecal samples obtained from the eastern Qinghai-Tibet Plateau, resulting in 6.51–12.72 Gb of raw data per sample. We successfully assembled 17 complete mitogenome sequences (~16,720 bp) and identified 67 SNPs. Phylogeographic analysis revealed two divergent mtDNA lineages with a patristic distance of 0.31%, comparable to the divergence observed between major lineages of lions (0.38%–0.82%) and tigers (0.24%–0.56%). One lineage was predominantly found in the Qilian Mountains, while the other was more broadly distributed across the Sanjiangyuan Region and the Hengduan Mountains. These results reveal a considerable level of mtDNA diversity at a local scale, which was missed in a previous study focusing on short mtDNA segments. Our study demonstrates the promising applicability of mitogenome assembly via NGS of fecal DNA, and we anticipate that it may advance global snow leopard conservation genetics by alleviating technical hurdles and enhancing data sharing.