Genetic drift and bottleneck do not influence diversity in Toll‐like receptor genes at a small spatial scale in a Himalayan passerine

Genetic diversity is important for long‐term viability of a population. Low genetic diversity reduces persistence and survival of populations and increases susceptibility to diseases. Comparisons of the neutral markers with functional loci such as immune genes [Toll‐like receptors; TLR] can provide useful insights into evolutionary potential of a species and how the diversity of pathogens and selection pressures on their hosts are directly linked to their environment. In this study, we compare genetic diversity in neutral (eleven microsatellite loci) and adaptive (seven TLR loci) loci to determine genetic variation in a nonmigratory western Himalayan passerine, the black‐throated tit (Aegithalos concinnus), distributed across an elevation gradient with varying degree of pathogen‐mediated selection pressure. We further compare the diversity in TLR loci with a high‐elevation sister species, the white‐throated tit (Aegithalos niveogularis). Our results indicate a lack of population genetic structure in the black‐throated tit and signatures of a past bottleneck. In contrast, we found high diversity in TLR loci and locus‐specific (TLR7) signatures of pathogen‐mediated selection, which was comparable to diversity in the white‐throated tit. Levels of diversity at TLR5 locus corresponded very closely with neutral microsatellite variation. We found evidence of positive selection in TLR1LA, TLR5, and TLR7 loci highlighting the importance in pathogen recognition. Our finding demonstrates that reduction in neutral variation does not necessarily lead to reduction in functional genetic diversity and probably helps in revival of population in a widespread species. Comparisons of allelic richness (size corrected) using eight neutral loci and seven TLR loci (*p