International Journal of Molecular Veterinary Research, 2025, Vol.15, No.1, 1-12 http://animalscipublisher.com/index.php/ijmvr 6 6.2 Influence of artificial selection on immune genes Artificial selection has extensively shaped the genetic foundation of the domestic dog, including their genes for the immune system. The intense trait-targeted selection during the process of domestication has led to the forthcoming rebuilding of genomic regulatory element structure and sequence with an eventual impact on immune function (Koch et al., 2016). Copy number variations (CNVs) and structural variations (SVs) have also been recognized as primary determinants of phenotypic variation and disease susceptibility in domestic dogs. For instance, CNVs in immune response gene-related regions have been found to differ largely among breeds, and this differentiation indicates that these parts have been under artificial selection to enhance some immune features (Serres-Armero et al., 2017; 2021). 6.3 Comparative analysis of wild vs. domestic canid immunity Comparative genomic analysis of domestic dogs and their wild counterparts, viz., wolves and raccoon dogs, reveals widespread distinction in immune genes. The personalized structural patterns and methylation observed in domestic dogs are not found in wild canids, and this points to the fact that domestication has led to unique immunogenetic profiles (Koch et al., 2016; Wang et al., 2018). For instance, MHC class I gene research in raccoon dogs demonstrates the extensive allelic diversity under positive pathogen selection, as in domestic dogs, to indicate long-term balancing selection in dogs (Bartocillo et al., 2021). In addition, genomic areas under selection in domestic dogs overlap with areas linked to immune response, reflecting the influence of natural and artificial selection on domestic dog immune systems (Plassais et al., 2019). 7 Comparative Genomics of Canids and Other Mammals 7.1 Insights from comparative studies with non-canid carnivores Comparative genomic investigations with non-canid carnivores have also provided useful insights into the evolution of immune system genes. MHC class I genes in the sable (Martes zibellina), for instance, revealed signs of balancing selection and recombination in their evolution. This study also reported a potential nonclassical MHC class I family in Carnivora that would have existed before the divergence of Caniformia and Feliformia approximately 52~57 million years ago (Zhao et al., 2020). Similarly, comparisons of the Leukocyte Receptor Complex (LRC) of certain of these carnivores, such as felids and mustelids, have shown that LRC structure is relatively conserved in them. However, felids and canids vary to some extent in terms of the LILR gene sub-region, exhibiting different evolutionary histories (Figure 3) (Jelínek et al., 2023). 7.2 Immune gene evolution across carnivoran lineages Immune gene evolution in carnivoran lineages is marked by extensive adaptation and diversity. In raccoon dogs (Nyctereutes procyonoides), the MHC class I genes have wide allelic diversity owing to pathogen-driven positive selection, recombination, and long-term balancing selection. The diversity is an indicator of the high frequency of non-synonymous substitutions and positively selected sites in the MHC class I protein domains (Bartocillo et al., 2021). Additionally, the rapid evolution of HERC6 and the doubling of a rodent- and bat-specific chimeric HERC5/6 gene suggest that the genes have experienced powerful adaptive evolution likely due to genetic arms races with viral pathogens (Jacquet et al., 2020). This rapid evolution is also observed in bats, in which reduction of interferon (IFN)-α genes and enlargement of IFN-ω genes may be contributing to their particular immune responses as well as heightened viral tolerance (Scheben et al., 2023). 7.3 Broader implications for mammalian immunity Comparative genomics between canids and other mammals is of great importance in the understanding of mammalian immunity. The occurrence of conserved and divergent immune gene families in all mammalian lineages indicates the complex evolution of the immune system. For example, the comparison of the opossum immune genome suggests that the increase in mammalian immune system complexity occurred before the marsupial-eutherian divergence, approximately 180 million years ago. This indicates that early mammals likely possessed all large immune gene families and lineage-specific expansion and contraction occurred under fluctuating pathogen pressures (Belov et al., 2007). Further, the evolutionary data gained by host-pathogen
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