International Journal of Molecular Evolution and Biodiversity, 2025, Vol.15, No.1, 10-28 http://ecoevopublisher.com/index.php/ijmeb 25 7 Concluding Remarks Comparative genomics has become a powerful tool to reveal the mysteries of Galliformes evolution. First, at the macro-evolutionary level, comparative genomics has helped reconstruct more reliable phylogenetic relationships among Galliformes species and clarified some evolutionary nodes that have long been in doubt. The phylogenetic tree constructed using whole genome data supports the monophyly and evolutionary order of the main groups of Galliformes, and provides a quantitative estimate of the time of differentiation in combination with the molecular clock. These achievements have elevated traditional taxonomy to the genomic scale and established a new paradigm for avian systematics. Secondly, in terms of species and lineage formation, comparative genomics captures the molecular traces of natural selection during domestication and differentiation. A series of gene variants related to domestication and yield traits have been identified, such as TSHR, IGF2BP1, SOX5, etc. Their discovery directly benefited from cross-group genome comparisons. Thirdly, at the level of functional gene evolution, genome comparisons of different Galliformes species revealed the conservation and variation of many gene families. For example, it was found that birds have a number of protein-coding genes comparable to mammals, but they are distributed on microchromosomes, which changed our previous understanding that the number of bird genes was underestimated. This information has broadened the knowledge boundaries of vertebrate genomics. It is particularly worth emphasizing that comparative genomics provides an evolutionary perspective for studying model species such as domestic chickens, putting them back into the wild lineage for examination, and thus obtaining answers to some long-standing unsolved questions. For example, the origin and spread of domestic chickens were revealed through large-scale genome sampling and comparison, and the picture of origin subspecies and multi-center diffusion was determined. Another example is the huge phenotypic difference between domestic chickens and wild types. By comparing the selection sweep of the whole genome, we know that the genetic factors behind them are so numerous and each has its own mechanism. It can be said that comparative genomics has built a bridge between macroevolution and microgenes. The discoveries made in the ideal system of Galliformes have not only enriched avian evolutionary biology, but also provided a model for the evolutionary research of other domestic animals and wild animals. As a typical representative of domesticated animals, the evolutionary dynamics of domestic chickens condense a microcosm of species adaptation to the human environment. By analyzing the changes in the genome before and after the domestication of domestic chickens, we can understand the species adaptation mechanism more broadly. First, the case of domestic chickens demonstrates the importance of pre-adaptive mutations: some mutations that are low-frequency in wild species (such as TSHR and yellow skin gene mutations) become advantageous in the new environment (domestic environment), and are therefore rapidly selected and fixed. This suggests that maintaining genetic diversity in wild populations is important for adaptation to potential environmental changes. Second, the domestication of domestic chickens reflects adaptation driven by rapid artificial selection. In just a few thousand years, domestic chickens have undergone significant changes in behavior, morphology, and physiology, and their speed far exceeds the rate of evolution under natural selection. This proves that the genome of a species has considerable plasticity and can reshape the phenotype through mutations in a few key genes under strong selection pressure. For example, only a SOX5 insertion can change the morphology of the comb, and an EDN3 duplication can make the skin darker. This reflects that there are certain "switch" nodes in the gene regulatory network, which have a large effect once mutated, opening up a shortcut for species adaptation. The evolutionary dynamics of domestic chickens show that gene flow and hybridization may play an active role in adaptation. During the process of spreading, domestic chickens have acquired additional beneficial mutations (such as disease resistance alleles of gray jungle fowl) by hybridizing with different wild jungle fowl, thus better adapting to different regional environments. This is consistent with the view that “hybridization promotes adaptation” found in more and more studies on wild species. When facing environmental stress, populations can expand their adaptability potential by introducing new mutations through hybridization. The multi-source background experienced by domestic chickens has given them a wide range of genetic diversity, enabling them to survive and reproduce in various climatic conditions around the world. This is also inspiring for current biodiversity conservation: maintaining moderate gene exchange or gene pool diversity between populations may improve their ability to cope with future environmental changes. Domestic chicken research also emphasizes the
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