International Journal of Molecular Evolution and Biodiversity, 2025, Vol.15, No.1, 10-28 http://ecoevopublisher.com/index.php/ijmeb 11 However, archaeological evidence shows that true domestication may have occurred in the middle and late Neolithic period thereafter. This suggests that the domestication of domestic chickens is a gradual process that may involve long-term genetic exchanges in wild populations and multi-stage domestication events. Similar phenomena are also reflected in other domestic animals: for example, the two main groups of domestic cattle have hybridized with closely related species such as yaks during their diffusion, thereby increasing genetic diversity and environmental adaptability (Li et al., 2017). Therefore, analyzing the signals of artificial selection and gene flow during domestication through large-sample whole-genome comparison has become an effective way to solve the mystery of the origin and evolution of domestic chickens. The chicken genome was first sequenced and published in 2004, pioneering the study of bird genomes. Since then, the rapid progress of sequencing technology has enabled the publication of high-quality genomes of multiple Galliformes species, laying the foundation for comparative genomics research. Through cross-species genome comparison, the conservation and variability of genome structure can be revealed, gene deletions or new events occurring in specific branches can be identified, and molecular markers of lineage differentiation and trait domestication can be detected in combination with population genetics analysis (Ouyang et al., 2022). As a model species, the rich variety and clear history of artificial selection of domestic chickens provide ideal materials for studying domestication selection using comparative genomic methods. For example, through pan-genome analysis, the shared and unique gene sets of different chicken breeds can be identified, thereby discovering genes and variants missed in the reference genome. For another example, the combination of genome-wide association analysis (GWAS) and selection scanning can locate loci that are strongly selected during the domestication and variety differentiation of domestic chickens. This study will systematically summarize the current status of comparative genomics research on Galliformes species, focusing on analyzing the dynamic changes in the genome and adaptive evolutionary mechanisms of chickens during domestication and breeding, comparing the genome characteristics of representative species of Galliformes, including assembly quality, chromosome composition and repeat sequences, reconstructing the phylogenetic relationship of Galliformes based on genomes, estimating the differentiation time of domestic chickens and closely related wild species, analyzing the selected genes related to speciation, and explaining the genome changes selected by humans during the domestication of chickens, such as the improvement of the genetic basis of phenotypic traits, changes in genetic diversity and genomic structural variation. By comparing the genomes of various East Asian chicken breeds in China, the genetic structure, domestication origin and adaptive genetic characteristics of local breeds are analyzed. Through multi-level comparative genomic research, this study hopes to provide a systematic review for understanding the evolutionary differentiation mechanism of Galliformes species and revealing the dynamics of chicken domestication, and provide a theoretical basis and data support for the formulation of future poultry breeding strategies. 2 Genome Features of Galliformes and Comparative Dataset 2.1 Sequenced representative species and assembly quality With the development of high-throughput sequencing and assembly technology, high-quality genome sequences of many representative species of Galliformes have been completed in recent years, thus constructing a comprehensive comparative data set. The reference genome of domestic chicken has been continuously improved since its first release. At present, the genomes of multiple breeds or individuals have been assembled with high precision, even including previously missing microchromosome sequences and complex repetitive regions. For example, Xu Luohao et al. constructed a complete genome map based on the Huiyang Bearded Chicken in China, supplementing the 6 microchromosomes and a large number of repetitive sequences missing from the reference genome. This complete assembly reconstructed the chromosomes of ancestral vertebrates and analyzed the centromere sequence of domestic chickens, which greatly promoted our understanding of the avian genome architecture (Huang et al., 2018). In addition to domestic chickens, the genomes of other Phasianidae species such as ring-necked pheasants (Phasianus colchicus), turkeys (Meleagris gallopavo) and quails (Coturnix japonica) have also been sequenced. Meng He et al. assembled a high-quality reference genome of pheasant through multi-platform assembly, with a genome size of about 0.99 Gb and 23 058 predicted protein-coding genes. The
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