International Journal of Molecular Evolution and Biodiversity, 2025, Vol.15, No.1, 10-28 http://ecoevopublisher.com/index.php/ijmeb 14 confirms that Gallus is a relatively early differentiated branch in the Phasianidae, and is quite different from other Phasianidae groups (such as Phasianus and Pavo). When constructing a genome phylogenetic tree, it is necessary to avoid interference from factors such as incomplete pedigree sorting (ILS). To this end, researchers used the co-alescent method and the method of sampling different gene segments to test controversial nodes. The family-level genome analysis of Stiller et al. (2024) showed that even with the whole genomes of 218 bird family representatives, some deep nodes still had a certain degree of gene tree inconsistency. Similar problems may also exist within the Galliformes due to ancient rapid radiation. With the improvement of data volume and analysis methods, the phylogenetic relationships of the main groups of Galliformes have been basically clarified. If ancient genome data can be introduced in the future, it is expected to further calibrate the branching time and detect traces of prehistoric hybridization, adding information of the time dimension to the phylogenetic tree. 3.2 Divergence times among chicken, junglefowl, and related taxa Accurately estimating the divergence time of domestic chickens and their closely related wild species will help to understand the spatiotemporal background and speed of domestic chicken domestication. Using the whole genome molecular clock method, Wang et al. (2020) used multiple statistical methods to infer the separation time of the domestic chicken lineage and the subspecies of red junglefowl. Among them, the divergence time between the domestic chicken and the G.g. spadiceus subspecies was about 9.5 thousand years ago (present), while the divergence with other red junglefowl subspecies (such as Javan junglefowl and Indian junglefowl) was earlier. It is worth noting that this estimate is not equivalent to the time when domestication actually began, because the specialized morphology and archaeological remains of domestic chickens appeared later after genetic separation. In fact, ancient DNA studies have found that some key alleles for domestic chicken domestication (such as TSHR gene mutations) did not increase rapidly in frequency in European domestic chickens until about 1 000 years ago. This suggests that after the initial domestication, the domestic chicken may have experienced a long period of free-range and slow evolution, and then, driven by the development of human civilization and breed improvement, more intense selection and differentiation occurred in the last one or two thousand years. For other species of Galliformes, phylogenetic and molecular clock analysis also gave a corresponding time frame. Ultra-conserved element analysis showed that the approximate radiation time of each genera of Phasianidae was around the middle Miocene 20 million years ago. The emergence of the Gallus gallus genus is speculated to be in the late Miocene, and then the various species of jungle fowl gradually differentiated in the Pliocene. By the Pleistocene (about 2 million years ago), several species of modern jungle fowl (red jungle fowl, gray jungle fowl, Ceylon jungle fowl, green jungle fowl) had each taken shape. This is basically consistent with the estimation of mitochondrial DNA. As a descendant of the red jungle fowl, the genome of the domestic chicken is highly similar to that of the wild type, and the differentiation time is short and occurred during the process of human domestication. Therefore, the genomic differences are mainly reflected in some artificial selection markers, rather than the overall large genetic distance. It is worth mentioning that some studies have tried to more accurately characterize the genomic composition of domestic chickens at different times through ancient genome methods. For example, a study measured the DNA of European domestic chicken bones about a few hundred years ago and found that the frequency of some domestication-related alleles (such as TSHR mutations) was significantly lower than that of modern domestic chickens. This directly confirms the role of modern selection in human breed improvement. Combining various evidences, the timeline of domestic chicken evolution can be outlined: red junglefowl have survived and reproduced in Southeast Asia and southern China for a long time. During the holocene environmental changes, one of the geographical populations began to associate with humans and was gradually domesticated and utilized around 6 000~5 000 BC (Cai et al., 2022). In the next few thousand years, domestic chickens spread to various parts of Eurasia with the spread of agriculture, and the indigenous chicken populations in different regions were genetically mixed with local red junglefowl or other junglefowl species to a certain extent (Guo et al., 2022). In the Middle Ages and modern times, people carried out targeted breeding for
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