Low genetic diversity of major histocompatibility complex class II DQB gene in wild rhesus and long-tailed macaques in Thailand reflects purifying selection and poses risks to population health

Rhesus (Macaca mulatta) and long-tailed (M. fascicularis) macaques, important for biomedical research, are distributed across Thailand, and hybridization and introgression between species influence genetic diversity, potentially leading to variability in traits and pathogen susceptibility. Elucidation of the genetic components directly related to pathogen susceptibility, such as major histocompatibility complex genes (MHC) across different environmental conditions, is crucial. Thus, this study examined the MHC class II DQB diversity in 18 populations of wild rhesus and long-tailed macaques in Thailand. Next-generation sequencing was used to screen 298 bp partial exon 2 of DQB. Habitat suitability was analyzed using Maximum Entropy Modeling to identify the main factors affecting macaque distribution, which may relate to allelic diversity. Six alleles (Mamu-Mafa-DQB1*TH01–Mamu-Mafa-DQB1*TH06) were observed in both species, with no evidence of species-specific alleles. Two alleles (Mamu-Mafa-DQB1*TH05 and Mamu-Mafa-DQB1*TH06) were restricted to two Northeastern populations. Selection analysis indicated that purifying selection acted on the MHC gene pool. Northeastern Thailand was identified as a suitable habitat for rhesus macaques, with the distance to roads as a primary predictor. Central to southern Thailand, with its elevation and distance to rivers, was predicted to be suitable for long-tailed macaques. The homozygous genotype of Mamu-Mafa-DQB1*TH02 allele was found in all individuals of one long-tailed macaque population, resulting in an increased risk of poor population health and pathogen infection. This study provides insights into the evolution of Thai macaques with potential implications for their use in biomedical research, such as disease susceptibility and resistance, as well as in vaccine development.