NUMTs as Diagnostic Markers for Hybrid Identification in Tigers: A Novel Reference-Free Approach
DOI:
https://doi.org/10.5281/zenodo.17386708Keywords:
Nuclear mitochondrial DNA (NUMTs), Hybrid identification, Panthera tigris altaica, Panthera tigris amoyensis, Gene pool contaminationAbstract
Maintaining genetic purity is critical in conservation breeding programs, especially for endangered subspecies like the South China tiger (Panthera tigris amoyensis) and the Amur tiger (Panthera tigris altaica), where hybridization threatens subspecies integrity and reintroduction success. However, identifying hybrids is challenging due to unreliable morphological traits and limited access to verified purebred genomes. Here, we present Auto-Ref HybrID, a novel reference-free method that leverages nuclear mitochondrial DNA segments (NUMTs) as genetic markers to distinguish purebred and hybrid individuals using whole genome sequencing (WGS) data. We analyzed 400 fecal samples from captive tigers and found that hybrid individuals exhibit significantly higher NUMT counts, elevated mutation rates, and greater divergence from the maternal mitogenome compared to purebreds. Genetic distance metrics and phylogenetic clustering confirmed the presence of hybridization signals, even at shallow sequencing depths. Our results establish NUMTs as robust, scalable markers for hybrid detection and demonstrate that Auto-Ref HybrID is a powerful tool for assessing gene pool contamination in conservation programs where reference genomes are lacking
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