International Journal of Molecular Evolution and Biodiversity, 2025, Vol.15, No.1, 29-39 http://ecoevopublisher.com/index.php/ijmeb 29 Review Article Open Access Evolutionary Dynamics of Mitochondrial and Nuclear Genomes in Geese: Implications for Phylogenetic Reconstruction Hongbo Liang, Jia Xuan Institute of Life Science, Jiyang College of Zhejiang A&F University, Zhuji, 311800, Zhejiang, China Corresponding author: jia.xuan@jicat.org International Journal of Molecular Evolution and Biodiversity, 2025, Vol.15, No.1 doi: 10.5376/ijmeb.2025.15.0003 Received: 20 Dec., 2024 Accepted: 26 Jan., 2025 Published: 09 Feb., 2025 Copyright © 2025 Liang and Xuan, 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: Liang H.B., and Xuan J., 2025, Evolutionary dynamics of mitochondrial and nuclear genomes in geese: implications for phylogenetic reconstruction, International Journal of Molecular Evolution and Biodiversity, 15(1): 29-39 (doi: 10.5376/ijmeb.2025.15.0003) Abstract Geese, due to their complex evolutionary history and multiple hybridization and domestication processes, have become an important model for studying the phylogeny and genomic evolution of birds. This study reviewed the research achievements on the evolution of mitochondrial and nuclear genomes in geese in recent years, explored the roles of these two types of genomes in speciation, lineage differentiation and trait domestication, and emphasized some factors affecting phylogenetic analysis, such as gene infiltration, incomplete lineage separation and inconsistency between mitochondrial and nuclear genomes. This study also summarized the origin, population structure and genetic diversity of Chinese domestic geese, and combined with case analysis, revealed the geographical distribution characteristics of mitochondrial haplotypes. This study hopes to provide a theoretical basis for a further understanding of the complex evolutionary process of geese and other waterfowl. Keywords Goose phylogeny; Mitochondrial and nuclear genomes; Genomic introgression; Lineage diversification; Domestication and genetic diversity 1 Introduction Geese belong to the genera Anser and Branta and are very important in the study of bird evolution. They have a relatively complete fossil record and have blazed a unique evolutionary path within the Anatidae family. The evolutionary history of geese is complex, featuring both rapid speciation processes and ancient hybridization events. Therefore, it serves as an excellent model for studying the genetic diversity and speciation mechanisms of birds. Although different species of the genus Anser have obvious differences in appearance and behavior, their kinship is actually very close, which makes their evolution more difficult to explain and also indicates that we need to use systematic genomic data to further clarify their relationships (Ottenburghs et al., 2017). Mitochondrial DNA (mtDNA) has a high mutation rate, is inherited only through the maternal line, and has a compact structure. It has always been applied in the phylogenetic research of birds and is also a commonly used molecular marker for reconstructing evolutionary relationships and species identification (Pacheco et al., 2011; Liu et al., 2013). However, the nuclear genome can also provide a lot of information that mtDNA cannot display, such as genetic recombination, incomplete separation of lineages and other evolutionary processes. These are all very crucial factors when studying the evolution of geese. The phylogenetic trees drawn from mitochondrial and nuclear genomes often show inconsistencies. Such inconsistencies are generally caused by hybridization, gene infiltration or incomplete lineage sequencing, which also indicates that it is necessary to integrate the two genomic data simultaneously (Ottenburghs et al., 2017; Princepe and De Aguiar, 2020; DeRaad et al., 2023). This study explored how the mitochondrial and nuclear genomes of geese evolved, with a focus on their roles in phylogenetic research. It analyzed the genetic differences, hybridization, and lineage division methods of these two genomes to illustrate the evolutionary relationships among different goose species, and also evaluated the reliability of different genetic markers in addressing phylogenetic issues. This study hopes to help researchers understand the evolutionary process of birds more comprehensively and provide better phylogenetic research methods for species groups with complex evolutionary histories.
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