International Journal of Molecular Evolution and Biodiversity, 2025, Vol.15, No.1, 29-39 http://ecoevopublisher.com/index.php/ijmeb 31 they might have been separated before and later had some gene exchanges. Ely et al. (2017) found that the mitochondrial differences among different populations of the white-fronted goose were quite obvious, which might be related to their loyalty to the breeding ground, population structure and the way resources were used. In China, the mitochondrial DNA of some local goose breeds is also very diverse. The diversity index (Hd) of some breeds exceeds 0.9, and gene exchange often occurs among different goose flocks. Qi et al. (2024) identified a total of 81 different haplotypes in their study, which were classified into six major groups. 3.3 Mitochondrial introgression across goose populations The evolutionary process of geese may have been influenced by the infiltration of mitochondrial genes, hybridization between different species, and the fact that their lineages have not yet been completely separated. The different species of the genus Goose do not match the evolutionary tree of mitochondria in terms of appearance, suggesting that several situations might be at play. Ancestors originally had multiple genetic types, hybridization occurred among different species, or they evolved similar appearances. Genetic exchange among some goose breeds in China is also relatively frequent, which further indicates the existence of genetic infiltration. Qi et al. (2024) hold that this situation might make the geographical distribution among different species unclear and also make it more difficult to reconstruct their evolutionary relationships. 4 Nuclear Genome Evolution and Diversity 4.1 Advances in nuclear genomic sequencing in geese By using advanced technologies such as PacBio, Bionano and Hi-C, researchers have completed the high-quality genome assembly of multiple goose breeds, such as the pink-footed goose and the lion-head goose. All these assemblies have reached the chromosomal level. And more than 20 000 protein-coding genes were identified (Jing et al., 2022; Zhao et al., 2022; Colom and O’Brien, 2024). These data have laid a very good foundation for subsequent genomic comparisons, adaptability studies, and the analysis of breed characteristics (Gao et al., 2016; Jing et al., 2022; Zhao et al., 2022). Jing et al. (2022) and Zhao et al. (2022) also conducted large-scale gene resequencing on nearly 1 000 geese, supporting the claim that “domestic geese have two ancestral sources”, and also identified many genetic markers related to important economic traits. 4.2 Genetic signals of domestication and breed differentiation Zhao et al. (2022) and Zhang et al. (2023) identified several candidate genes related to growth, reproduction, and morphological characteristics, such as TGFBR3L, CMYA5, FOXD1, ARHGEF28, SUCLG2, LDLRAD4, and GPR180. The allele frequencies of some genes increased rapidly under the influence of artificial selection. For instance, when people specifically selected geese with white feathers, some common gene types in domestic geese were formed (Figure 1) (Jing et al., 2022). Jing et al. (2022) and Zhang et al. (2023) found that compared with European geese, local goose breeds in China have higher genetic diversity. Gene exchange often occurs among different breeds, and gene infiltration makes the differences between breeds more obvious. 4.3 Gene flow and incomplete lineage sorting Genome-wide analyses have found that in the genera Anser and Branta, there were early and modern hybridization events, which made their evolutionary relationship as complex as a web, and mixed structures also emerged in the genome (Ottenburghs et al., 2017). Wilson et al. (2022) and Zhang et al. (2023) found that there was also a considerable amount of gene infiltration among domestic geese, and some small genetic aggregations occurred within certain populations, indicating that both the natural environment and human selection have jointly influenced the current genetic structure of geese. Incomplete phylogenetic differentiation is the result of many geese rapidly forming new species, which makes their evolutionary relationships more difficult to understand. Ottenburghs et al. (2017) proposed that to solve these problems, more advanced statistical methods and network models need to be used to distinguish which are caused by hybridization and which are due to a common ancestor.
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