Beyond neutral loci: Examining immune gene variation in tigers (Panthera tigris)

Genetic vulnerability of wild populations is generally assessed using neutral loci, which may not accurately reflect a populations adaptive potential. In contrast, diversity at loci putatively involved in fitness and survival, such as immune genes, could be a better proxy for future survival. Research on immune genes in wild species has traditionally focused on the MHC loci. We investigate five families of non-MHC immune genes -Tumor Necrosis Factor, Interleukin, Toll-like Receptor, Leukocyte Immunoglobulin-Like Receptors, and Chemokine - involved in adaptive and innate immunity in the tiger (Panthera tigris), an endangered carnivore. We compare immune gene diversity to neutral diversity using publicly available resequenced whole genomes from 107 tigers representing all extant subspecies and subpopulations (within India) with different demographic histories. Immune receptor genes show high nucleotide diversity (mean: 0.0019) compared to neutral loci (0.0008) and immune signalling genes (0.0004), suggesting positive selection. However, heterozygosity of immune genes does not differ significantly from neutral loci, suggesting strong genetic drift. Populations with histories of bottleneck and inbreeding show reduced genetic diversity and high mutation load but some immune loci retain polymorphisms even in inbred populations. Genetic differentiation and site frequency spectra of immune loci correspond to patterns from neutral loci but Toll-like receptor genes show signatures associated with balancing selection. Our findings indicate that genetic drift is likely the predominant evolutionary force shaping genetic variation in bottlenecked endangered species such as tigers, even at immune loci that are typically subject to selection. However, remnants of past balancing selection might preserve important variation, potentially influencing population survival.