International Journal of Molecular Evolution and Biodiversity, 2025, Vol.15, No.1, 10-28 http://ecoevopublisher.com/index.php/ijmeb 13 different transposon expansion histories. For example, analysis of the ring-necked pheasant genome found that the CR1 subfamily common in some chickens has fewer copies in pheasants, while some elements of DNA transposons are relatively abundant. This may be related to species-specific genomic defense mechanisms or population history. In addition, the abundant endogenous viral sequences on the W chromosome of domestic chickens may have an impact on female physiology and interspecific hybrid infertility. In addition to repetitive sequences, regulatory elements in the genome (such as enhancers and promoters) are also changing in evolution. Comparative genomes can identify conserved non-coding sequences and predict the loss or creation of functional regulatory elements. Studies have shown that despite the early divergence between bird orders, there are cross-species conserved enhancer clusters near multiple development-related genes. However, some regulatory sequences have also undergone significant lineage-specific changes in Galliformes. For example, compared with turkeys, domestic chickens may lack a conserved sequence upstream of feather development genes, suggesting that the loss of these elements may be related to the feather traits of specific breeds (Ouyang et al., 2022). For another example, structural variations or insertions have been found near the promoters of hormone receptor genes that regulate growth and reproduction in different chicken breeds, which may be regulatory changes caused by artificial selection. With the progress of multi-species pan-genome and map comparisons, scientists have begun to draw a picture of the evolution of regulatory elements in the genomes of Galliformes birds, including which sequences are highly conserved and functionally important, and which sequences have mutated, deleted or newly formed in specific lineages. Overall, comparative analysis of genomic repeat sequences and regulatory elements reveals the mechanism by which the genomes of Galliformes species achieve adaptive evolution through detailed changes while maintaining overall stability, providing clues for further exploring the genetic basis of trait differences. 3 Phylogeny and Species Divergence 3.1 Whole-genome-based phylogenetic tree reconstruction The use of whole genome data for phylogenetic reconstruction has become an effective means to determine the evolutionary relationship of birds. Traditionally, systematic classification studies have been conducted on Galliformes based on mitochondrial DNA or a few nuclear gene sequences, but the results are uncertain due to factors such as inconsistencies between gene trees and species trees and hybridization. With the help of high-throughput genome sequencing, researchers can obtain whole-genome SNPs or colinear sequences of many species of Galliformes to construct high-resolution phylogenetic trees. Kimball et al. (2021) collected ultraconserved element (UCE) sequence data of 130 species of Galliformes birds and constructed a large-scale phylogenetic supermatrix containing all genera. The resulting internal phylogenetic tree is basically consistent with the previous results based on mitochondria, but with higher resolution and stronger support. The overall topology shows that the branches within the Phasianidae (including chickens, pheasants, peacocks, etc.) are clearly differentiated, for example, the genus Phasianus and the genus Gallus are grouped separately; and the positions of subfamily groups such as partridges and bamboo partridges are also more reliably determined. These big data analyses based on the whole genome help to solve evolutionary nodes that were previously difficult to determine. A significant finding is that several major lineages of modern chickens form two large branches on the whole genome phylogenetic tree: one is the domestic chicken breeds in northern Eurasia and their closely related wild types, and the other is the local native chickens in central and southern China. Before the emergence of these two major lineages, some earlier differentiated domestic chicken individuals mainly came from southwest China and Southeast Asia. This result supports the possibility that there may be multiple early domestication centers or diffusion paths for domestic chickens, rather than simple diffusion after a single origin. This is consistent with the comprehensive analysis of nuclear DNA and mitochondrial evidence, suggesting that domestic chickens have undergone a complex migration and hybridization process after domestication. In contrast, the subspecies of red jungle fowl all form monophyletic groups on the genome tree, and are clearly differentiated from each other. This means that the pedigree structure of wild jungle fowl is relatively stable, while domestic chickens have mixed multiple genetic components due to artificial propagation. The cross-species genome phylogenetic tree also
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