Bioscience Evidence 2025, Vol.15, No.5, 209-218 http://bioscipublisher.com/index.php/be 211 chickens have been independently domesticated many times in South Asia and Southeast Asia. After whole genome sequencing, haplogroups could be further classified and complex mixtures between domestic chicken and red pheasant lineages were observed (Liu et al., 2006; Yw et al., 2012; Hata et al., 2021) (Figure 1). In the research of local breeds, mtDNA is also often used to trace the origin and genetic diversity of domestic chickens (Huang et al., 2017; Boudali et al., 2020; Liu et al., 2020). 3.2 Nuclear DNA markers Nuclear DNA markers can provide more information, including population structure, breed differences and trait changes. Studies of microsatellites and SNPS have shown that both domestic chickens and pheasants have high genetic diversity and complex population structures (Hata et al., 2021; Larkina et al., 2021). Some gene loci, such as NCAPG-LCORL, BCO2 and TSHR, are closely related to the production traits and appearance differences of poultry, and therefore are very important in molecular breeding and systems research (Rubin et al., 2010; Qanbari et al., 2019; Larkina et al., 2021). Nuclear DNA data also revealed that there was gene infiltration and hybridization between domestic chickens and various pheasants, which enriched the genetic background of domestic chickens (Sawai et al., 2010; Lawal et al., 2019; Wang et al., 2020; Zhao et al., 2024). 3.3 Whole-genome sequencing (WGS) Whole-genome sequencing technology has enabled more detailed research on the evolution of domestic chickens and pheasants. WGS can detect tens of millions of SNPS and structural variations, and can also systematically identify selection signals, gene rearrangements and functional gene changes (Rubin et al., 2010; Qanbari et al., 2019; Wang et al., 2020; Wang et al., 2021). By analyzing a large number of samples worldwide, researchers have found that domestic chickens have multiple origins, complex gene exchanges, have also experienced domestication bottlenecks, and have an impact on genetic burden. WGS also identified gene regions related to growth, immunity and reproduction, providing new evidence for poultry breeding and conservation (Wu et al., 2023). 4 Evolutionary Traits Shaped by Domestication 4.1 Morphological traits Compared with wild free-range chickens, domestic chickens have more significant differences in appearance, mainly reflected in their body size, feather color and skull structure. Research has found that the skull changes of domestic chickens are more obvious than those of wild purebred chickens, especially in the areas where the neural crest originates, such as the protrusion of the skull of the crown-top chicken. This indicates that manual selection has a significant impact on appearance and functionality (Stange et al., 2018; Nunez-Leon et al., 2021). In addition, domestic chickens vary greatly in size, weight and feather color. Different breeds often correspond to different uses, such as laying eggs, producing meat or for ornamental purposes (Li et al., 2019; Larkina et al., 2021; Wang et al., 2021). 4.2 Physiological traits Domestic chickens differ from wild free-range chickens in terms of metabolism, reproduction and adaptation. The most typical example is the selection of the TSHR gene, which affects metabolic and reproductive rhythms. Domestic chickens generally no longer have strict seasonal breeding like wild breeds (Rubin et al., 2010; Lawal and Hanotte, 2021). In addition, domestic chickens also show different abilities in terms of growth rate, egg production, high-altitude tolerance and heat tolerance, which are closely related to some genetic variations (such as IGF2BP1, LEPR) (Li et al., 2019; Qanbari et al., 2019; Wang et al., 2021). 4.3 Behavioral traits Domestication has brought about significant changes in the behavior of domestic chickens. Domestic chickens are generally less afraid of humans, have lower aggression and are more sociable, all of which are regarded as manifestations of "domestication syndrome" (Belteky et al., 2018; Mehlhorn and Caspers, 2021). Experimental studies have found that as long as low fear is selected for five consecutive generations, it will lead to differences in behavior and hypothalamic DNA methylation, suggesting that behavioral evolution may be closely related to
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