Bioscience Evidence 2025, Vol.15, No.5, 209-218 http://bioscipublisher.com/index.php/be 210 This study compiles the new progress in the research on the evolution of domestic chickens and pheasants in recent years. The key points include: systematic relationships of the genus Gallus and evidence of multi-source domestication of domestic chickens; The roles of mtDNA, SNPs, microsatellites and nuclear DNA in the study of evolution and trait differentiation; The main findings of domestic chickens and pheasants in terms of genetic diversity, selection signals, gene exchange and adaptive evolution. At the same time, the application of these tools in the genetic improvement and protection of poultry was also prospected. Through these analyses, this study hopes to provide assistance in understanding the evolutionary mechanisms and genetic basis of domestic chickens, and also offer references for the protection and utilization of poultry resources. 2 Evolutionary Context of Chickens 2.1 Origin and diversification of junglefowls (Gallus gallus, G. sonneratii, G. lafayettii, G. varius) There are four wild chicken species in the genus Gallus: the red jungard (Gallus gallus), the gray jungard (G. sonneratii), the Ceylon jungard (G. lafayettii), and the green jungard (G. varius). Studies show that the red pheasant is the main ancestor of domestic chickens. However, grey, Ceylon and green pups have also contributed to the genetic diversity of domestic chickens (Sawai et al., 2010; Lawal et al., 2019; Wang et al., 2020; Zhao et al., 2024). Phylogenetic analysis revealed that the grey Grouse is more closely related to the Ceylon grouse. Together, they form a sister group and are also closely related to the red Grouse, while the green Grouse was the first to differentiate (Lawal et al., 2019). In terms of distribution, the red grouse is mainly found in South and Southeast Asia, the grey grouse in southern and western India, the Ceylon grouse only in Sri Lanka, and the green grouse in Java and surrounding islands of Indonesia (Zhao et al., 2024). There is gene exchange among these species, especially gene infiltration between the grey pheasant and domestic chickens, which has an impact on the appearance and adaptability of domestic chickens (Lawal et al., 2019; Zhao et al., 2024). 2.2 Timeline of domestication (~8 000 years ago in Southeast Asia) Both archaeological and molecular studies have shown that the domestication of domestic chickens began approximately 8,000 years ago during the Neolithic Age, mainly in Southeast Asia and Southwest China (Yw et al., 2012; Lorenzo et al., 2015; Lawal et al., 2019; Wang et al., 2020; Hata et al., 2021). The earliest domestication center was in the distribution area of the spadiceus subspecies of the red pheasant, which is today's southwestern China, northern Thailand and Myanmar. After that, humans brought domestic chickens to Southeast Asia, South Asia and other places . Archaeological sites and ancient DNA analysis support the claim that domestic chickens were independently domesticated in many places in Southeast Asia, and also indicate that domestic chickens were used for religion, rituals and food very early. 2.3 Phylogeographic insights into chicken domestication and migration Phylogenetic and distribution studies have shown that the domestication and spread process of domestic chickens is very complex. Mitochondrial DNA and whole-genome analysis revealed that there was a mixture of maternal lines and genomes among multiple subspecies of domestic chickens and red pheasants, and domestic chickens in different regions also had their own haplotypes and gene penetration patterns (Yw et al., 2012; Lorenzo et al., 2015; Lawal et al., 2019; Wang et al., 2020; Hata et al., 2021). The study also found fragments of grey Grouse, Ceylon Grouse and green Grouse in the genomes of domestic chickens, among which the genes of grey Grouse are directly related to the yellow skin of domestic chickens (Lawal et al., 2019; Zhao et al., 2024). The migration routes of domestic chickens are closely related to human activities. Archaeological evidence shows that about 2 250 years ago, domestic chickens crossed the Wallace Line with human migration and entered Indonesia and Pacific islands (Meijer et al., 2022). In East Asia, South Asia and the Pacific region, domestic chickens have gradually developed many different local breeds. 3 Phylogenetic Markers and Methodological Advances 3.1 Mitochondrial DNA (mtDNA) markers Mitochondrial DNA is commonly used in the origin studies of domestic chickens and pheasants, with the D-loop region and COI gene being the most common. Because it is inherited only through the maternal line and changes rapidly, it is very suitable for systematic analysis. Research has found that domestic chickens have multiple maternal origins and independently formed haplotypes in different parts of Asia. This indicates that domestic
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