Beyond neutral loci: Understanding immune gene variation in an endangered big cat
by BV Aditi | Uma Ramakrishnan | National Centre for Biological Sciences-TIFR | National Centre for Biological Sciences-TIFR
Abstract ID: 83
Event: The 3rd AsiaEvo Conference
Topic: Genomic diversity in nonequilibrium populations
Presenter Name: BV Aditi

Habitat fragmentation is a significant threat to wild populations worldwide, leading to increased isolation and inbreeding, loss of genetic diversity and increased extinction risk. Carnivores, owing to their ecology, are particularly susceptible to the consequences of habitat fragmentation. While previous studies have focused on neutral loci to assess genetic diversity, such loci may not provide an accurate prediction of a population's adaptive potential. In contrast, loci known to be involved in fitness can offer insights into the adaptive potential of isolated carnivore populations.

We assess genetic diversity and possible selection acting on non-MHC immune genes, which are known to be involved in immunity, but are less studied than MHC loci.  Using tigers as a model system for wild, endangered carnivores with low neutral genetic variation, we mine whole genome resequencing data from 120 range-wide genomes to examine patterns of genetic variation for non-MHC immune genes.

We identified variants in five families of innate and adaptive immune genes.  Our findings contrast immune gene diversity at receptor and signaling genes with neutral loci and in populations of different sizes and connectivity. We find that Toll-Like Receptor genes have the highest diversity amongst the gene families examined. Amur tigers have the lowest diversity at adaptive loci whereas South China and Indo Chinese tigers have the highest diversity. We also identified mutations that could be deleterious and highlight populations that carry a high frequency of such mutations, results of potential significance to management.