Selection and demography drive range-wide patterns of MHC-DRB variation in mule deer

Abstract

Background Standing genetic variation is important especially in immune response-related genes because of threats to wild populations like the emergence of novel pathogens. Genetic variation at the major histocompatibility complex (MHC), which is crucial in activating the adaptive immune response, is influenced by both natural selection and historical population demography, and their relative roles can be difficult to disentangle. To provide insight into the influences of natural selection and demography on MHC evolution in large populations, we analyzed geographic patterns of variation at the MHC class II DRB exon 2 locus in mule deer (Odocoileus hemionus) using sequence data collected across their entire broad range. Results We identified 31 new MHC-DRB alleles which were phylogenetically similar to other cervid MHC alleles, and one allele that was shared with white-tailed deer (Odocoileus virginianus). We found evidence for selection on the MHC including high dN/dS ratios, positive neutrality tests, deviations from Hardy–Weinberg Equilibrium (HWE) and a stronger pattern of isolation-by-distance (IBD) than expected under neutrality. Historical demography also shaped variation at the MHC, as indicated by similar spatial patterns of variation between MHC and microsatellite loci and a lack of association between genetic variation at either locus type and environmental variables. Conclusions Our results show that both natural selection and historical demography are important drivers in the evolution of the MHC in mule deer and work together to shape functional variation and the evolution of the adaptive immune response in large, well-connected populations.

Research Note: Possible influence of thermal selection on patterns of HSP70 and HSP90 gene polymorphisms in Thai indigenous and local chicken breeds and red junglefowls

“…Conversely, both the ω value and selective sweep analysis of HSP90 indicated the probability that Thai indigenous and local chicken breeds, as well as red junglefowls, have experienced balancing selection, consistent with the results of microsatellite analysis. The disparate genetic divergent patterns between the 2 thermotolerance-related genes, HSP70 and HSP90 , are likely driven by different selection modes ( Cook et al, 2022 ). The results of the present study suggest that purifying selection for thermal stress is common in Thai indigenous and local chicken breeds.…”

“…The paired-end 250-bp reads on the Illumina NovaSeq 6,000 platform were evaluated using FASTQC version 0.12.0, as described by Cook et al (2022) , to determine the quality of reads with a quality score above 20. The reads were merged using the “interleave” function in Python3 software.…”

“…The merged sequences were demultiplexed to obtain individual sequences within each pool using the “grep” command in Linux. Sequence clustering, filtering, allele assignment, and allele sequence checking were performed as described by Cook et al (2022) . Heat shock protein 70 and HSP90 genotypes were determined by comparing the number of reads for each genotype to the total number of reads.…”

“…The average amount of synonymous ( d S ) and non-synonymous ( d N ) substitutions per site was estimated according to the Nei–Gojobori's method with Jukes–Cantor correction, and a Z -test was then carried out to assess the d N / d S ( ω ) ratio as described previously in Cook et al (2022) . To further investigate the possible selection of HSP70 and HSP90 , neutrality tests, including Tajima's D , Fu's F , Fu and Li's F *, and Fu and Li's D * were performed following Cook et al (2022) . A selective sweep investigation was performed, as described by Budi et al (2023) .…”