International Journal of Molecular Evolution and Biodiversity, 2025, Vol.15, No.1, 10-28 http://ecoevopublisher.com/index.php/ijmeb 15 cockfighting, viewing and high yield purposes, which accelerated the differentiation between different strains. Therefore, the formation of genetic diversity in modern domestic chickens is a complex process that includes slow domestication in prehistoric times, migration and hybridization in historical periods, and recent artificial breeding. The estimation of the differentiation time of the whole genome provides us with a starting point, and further detailed characterization requires a comprehensive perspective combining archaeology, historical documents, and functional genomics research. 3.3 Core gene sets under selection during speciation Speciation involves the generation of isolation mechanisms and the accumulation of adaptive differences. Among Galliformes, different species have their own characteristics in ecological niches, behaviors, and morphology. Genomic studies can help find gene groups associated with these differences. Comparing recently differentiated closely related species (such as domestic chickens and red junglefowl subspecies) is an effective strategy for finding selected genes. Through whole genome scanning, Wang et al. (2020) identified a group of core genes that may have been selected during the differentiation of domestic chickens and red junglefowl. These include several genes related to reproductive development, such as changes in the expression regulation of SLC family genes in testicular development. These genes themselves have not undergone non-synonymous mutations, but show signals of selection loss in the domestic chicken population, indicating that selection may target their regulatory regions. The thyroid hormone receptor gene TSHR is a known marker of domestication in chickens. It encodes the thyroid stimulating hormone receptor and plays a role in seasonal reproductive regulation. A mutation in the TSHR gene that causes an amino acid substitution (Gly558Arg) is nearly fixed in domestic chickens, but is extremely rare in wild jungle fowl. This mutation is believed to reduce the reproductive response of domestic chickens to seasonal sunlight, allowing them to lay eggs and reproduce throughout the year. Ancient DNA studies have confirmed that the TSHR mutation became common in European domestic chickens in the Middle Ages, suggesting that this mutation was strongly artificially selected after it spread in domestic chickens. Interestingly, the natural frequency of this mutation in the ancestral subspecies of domestic chickens (G. g. spadiceus) is also not low (about 94%), suggesting that humans may have preferentially domesticated wild populations carrying this favorable mutation, thus laying the foundation for later domestication. This reflects the importance of "pre-adaptive" genetic variation in the process of speciation and domestication. At a higher level of comparison, different Galliformes species show their own unique adaptive characteristics, and selection has shaped the corresponding genomic differences. For example, the ring-necked pheasant has significant sexual dimorphism and complex feathers. Comparative genomic analysis found that genes related to calcium ion signaling and feather coloring in its genome may have undergone accelerated evolution. The study also found a large rearrangement in the MHC gene region of pheasants, speculating that the evolution of its immune system was driven by disease selection pressure. Another example is that guinea fowl (Numididae) may have different selection patterns for water metabolism and heat regulation genes compared to pheasant species living in arid environments in Africa. Studies have reported that genes that control feather coverage and skin evaporation in the guinea fowl genome show signs of positive selection (Ouyang et al., 2022). In addition, strains with extreme traits, such as “naked neck chickens” (no feathers on the neck), are believed to originate from mutations in the FGF20 gene; “curly feather chickens” (curled feather shafts) are related to loss-of-function mutations in the keratin gene KRT75. These mutations may have been extremely rare in wild species at first, but they were fixed under artificial selection, demonstrating the strong influence of humans on specific traits during species formation. 4 Genomic Dynamics of Chicken Domestication 4.1 Human-driven selection and its molecular impact on phenotypes Human selection played a decisive role in the evolution of domestic chickens from wild jungle fowl. In order to meet different production and aesthetic needs, humans exerted directional selection pressure on many traits of domestic chickens during domestication and subsequent breed improvement, including docile temperament, higher meat and egg production performance, and diverse appearance characteristics (Cai et al., 2022). These selections significantly changed the phenotype of domestic chickens in a short time scale dominated by humans,
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