International Journal of Molecular Evolution and Biodiversity, 2025, Vol.15, No.1, 10-28 http://ecoevopublisher.com/index.php/ijmeb 10 Research Insight Open Access Comparative Genomics of Galliformes and the Evolutionary Dynamics of Domesticated Chickens Jun Wang, Qibin Xu Animal Science Research Center, Cuixi Academy of Biotechnology, Zhuji, 311800, Zhejiang, China Corresponding author: qibin.xu@cuixi.org International Journal of Molecular Evolution and Biodiversity, 2025, Vol.15, No.1 doi: 10.5376/ijmeb.2025.15.0002 Received: 10 Dec., 2024 Accepted: 14 Jan., 2025 Published: 24 Jan., 2025 Copyright © 2025 Wang and Xu, This is an open access article published under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Preferred citation for this article: Wang J., and Xu Q.B., 2025, Comparative genomics of galliformes and the evolutionary dynamics of domesticated chickens, International Journal of Molecular Evolution and Biodiversity, 15(1): 10-28 (doi: 10.5376/ijmeb.2025.15.0002) Abstract Galliformes birds include pheasants, partridges, quails, turkeys, etc., which are relatively primitive and diverse groups on the avian evolutionary tree. In recent years, with the development of high-throughput sequencing and comparative genomics, a large number of Galliformes genomes have been analyzed, providing an unprecedented opportunity for in-depth study of their phylogenetic relationships, domestication history and functional gene evolution. This study reviews the basic characteristics of Galliformes genomes and cross-species comparative datasets, summarizes the latest phylogenetic analysis results and species divergence time estimates, and focuses on the dynamic changes in the genome of domestic chicken (Gallus gallus domesticus) during domestication, including the reshaping of genetic diversity, gene introgression from wild relatives, and genomic selection pressure caused by artificial breeding. The evolutionary trajectories of functional genes related to important economic traits of domestic chickens are further compared, and the key gene variations and their origins that affect the appearance, behavior, physiology and other traits of domestic chickens are listed. Finally, the progress of regional comparative genomic research is discussed using the East Asian domestic chicken lineage as an example, revealing the genetic structure of Chinese native breeds, evidence of multi-origin domestication and adaptive evolution mechanisms. This study uses systematic comparative genomic analysis to reveal the evolution of Galliformes genomes and the molecular mechanisms behind chicken domestication, providing a theoretical basis and reference framework for poultry breeding and resource protection. Keywords Galliformes; Comparative genomics; Phylogeny; Chicken domestication; Functional gene evolution 1 Introduction Galliformes is an ancient and diverse group in the class Aves, including Phasianidae, Turkey Family, Guinea Fowl Family, etc., with a total of more than 300 bird species. In the phylogenetic tree of birds, Galliformes and Anseriformes together form a basal new bird evolutionary lineage (i.e., land birds in the present-day jaws), which is considered to be a group that radiated rapidly near the Cretaceous-Paleogene mass extinction. The representative species of Galliformes, the domestic chicken (Gallus gallus domesticus), evolved from the red junglefowl and is one of the earliest domesticated animals by humans, and is widely raised around the world. The domestic chicken not only has important economic value, but is also a model organism, playing a key role in developmental biology, immunology and genetics research (Lawal et al., 2020). In recent years, with the development of sequencing technology, the genome sequences of domestic chickens and their closely related wild species have been continuously improved, and high-throughput comparative genomics has provided a new means for studying avian evolution. The origin and domestication process of the domestic chicken have long been controversial. The traditional view is that domestic chickens originated from the red junglefowl in Southeast Asia based on morphology and archaeological records, but there are different opinions on the specific time and place of domestication. Molecular systematic studies have gradually clarified this issue: large-scale analysis using whole genome variation data shows that all domestic chickens are phylogenetically clustered into a monophyletic group, and the closest wild relative is a specific subspecies of red junglefowl-Gallus gallus spadiceus in Myanmar and South China. Molecular clock calculations show that domestic chickens diverged from this subspecies about 9 500 ± 3 300 years ago, which roughly coincides with the period of climate warming in the Holocene (Wang et al., 2021).
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