Genetic diversity of Formosan pangolins (Manis pentadactyla pentadactyla) in Taiwan based on the MHC gene

Abstract

Abstract The Formosan pangolin (Manis pentadactyla pentadactyla) is an endangered species in Taiwan. The polymorphisms at major histocompatibility complex (MHC) gene regions could provide an indicator for immunological fitness and genetic diversity of a population. In this study, seven different novel markers for MHC genotyping of Formosan pangolin were developed and used to evaluate the genetic diversity of 92 Formosan pangolins. In the MHC markers, six loci showed monomorphism or only two haplotypes. Only one marker, a DLA class II DR-1 beta chain-like locus, showed more diversity: four haplotypes were detected and their relative frequencies were 62.0, 37.0, 0.5 and 0.5%, with nine polymorphic sites in the nucleotide sequence and six variable sites in the amino acid sequence. The non-synonymous substitution rate (dN) and synonymous substitution rate (dS) were 0.026 and 0.017, and showed that this locus appears to be under positive selection (dN /dS >1). Observed heterozygosity (HO) and expected heterozygosity (HE) were 0.413 and 0.482, respectively. FIS was 0.144, indicating that the population might have an inbreeding tendency (FIS > 0). Haplotype diversity (h) was 0.482 and nucleotide diversity (π) was 0.010. Overall, the results indicated that the genetic diversity of MHC genes among Formosan pangolins in Taiwan was insufficient.