MHC class II DQB diversity in the Japanese black bear, Ursus thibetanus japonicus

Abstract

BackgroundThe major histocompatibility complex (MHC) genes are one of the most important genetic systems in the vertebrate immune response. The diversity of MHC genes may directly influence the survival of individuals against infectious disease. However, there has been no investigation of MHC diversity in the Asiatic black bear (Ursus thibetanus). Here, we analyzed 270-bp nucleotide sequences of the entire exon 2 region of the MHC DQB gene by using 188 samples from the Japanese black bear (Ursus thibetanus japonicus) from 12 local populations.ResultsAmong 185 of 188 samples, we identified 44 MHC variants that encoded 31 different amino acid sequences (allotypes) and one putative pseudogene. The phylogenetic analysis suggests that MHC variants detected from the Japanese black bear are derived from the DQB locus. One of the 31 DQB allotypes, Urth-DQB*01, was found to be common to all local populations. Moreover, this allotype was shared between the black bear on the Asian continent and the Japanese black bear, suggesting that Urth-DQB*01 might have been maintained in the ancestral black bear population for at least 300,000 years. Our findings, from calculating the ratio of non-synonymous to synonymous substitutions, indicate that balancing selection has maintained genetic variation of peptide-binding residues at the DQB locus of the Japanese black bear. From examination of genotype frequencies among local populations, we observed a considerably lower level of observed heterozygosity than expected.ConclusionsThe low level of observed heterozygosity suggests that genetic drift reduced DQB diversity in the Japanese black bear due to a bottleneck event at the population or species level. The decline of DQB diversity might have been accelerated by the loss of rare variants that have been maintained by negative frequency-dependent selection. Nevertheless, DQB diversity of the black bear appears to be relatively high compared with some other endangered mammalian species. This result suggests that the Japanese black bears may also retain more potential resistance against pathogens than other endangered mammalian species. To prevent further decline of potential resistance against pathogens, a conservation policy for the Japanese black bear should be designed to maintain MHC rare variants in each local population.

Patterns of Adaptive and Neutral Diversity Identify the Xiaoxiangling Mountains as a Refuge for the Giant Panda

“…Here, higher d N / d S ratios were observed in the ABS of 6 Aime- MHC alpha and beta genes (Table 3), which is in accordance with published data on beta genes in bears [54], [58], [66] and other mammals [67], [68].…”

“…However, the d N / d S value in the ABS of DRB was higher than that of the giant panda DRB3 (5.084 vs. 2.176). In the black bear [58], the d N / d S value was also lower than that of Aime- DQB1 (1.48 vs. 3.500).…”

“…In the brown bear [54], there was evidence of positive selection at DRB with an ω estimate of 12.181 (giant panda DRB3, ω = 3.081); however, no signal positive selection was detected at DQB, which is the opposite of what was observed in the giant panda DQB loci (ω = 15.996 for DQB1, ω = 10.250 for DQB2). In the black bear [58], the ω estimate of 5.71 at DQB was lower than that of the giant panda. Bayesian analysis identified different numbers of codons under positive selection at Aime -MHC class II loci (6 for DQA1, 4 for DQA2, 6 for DQB1, 7 for DQB2, and 7 for DRB3).…”

Molecular polymorphism of MHC-DRB gene and genetic diversity analysis of captive forest musk deer (Moschus berezovskii)

“…Many endangered species, which exhibited low MHC polymorphism, were known to have gone through severe population bottlenecks (Blankenburg et al, 2003;Miller et al, 2008). However, several species have high MHC diversity despite severe population bottlenecks (Aguilar et al, 2004;Yasukochi et al, 2012), and some species experienced population expansion despite low MHC diversity, such as moose (Alcesalces), musk ox, roe or fallow deer (Mikko and Andersson, 1995).…”

“…Populations show low levels of MHC variation are expected to be more susceptible to detrimental pathogens and parasites (Sin et al, 2014), and as a result, demographic decline follows (Lochmiller and Deerenberg, 2000). Many endangered species exhibited low MHC polymorphism were known to have gone through severe population bottlenecks (Blankenburg et al, 2003;Yasukochi et al, 2012). Due to potentially low MHC diversity, some species (e.g.…”