International Journal of Molecular Evolution and Biodiversity, 2025, Vol.15, No.1, 29-39 http://ecoevopublisher.com/index.php/ijmeb 35 occurs, and there are also cases where mitochondria and nuclear genes are introduced together, indicating that they work in concert during the evolutionary process. The co-evolution between mitochondrial and nuclear genes is a key mechanism that drives wild animals and domestic species to adapt to the environment and differentiate into different lineages, which is of great significance for the evolutionary study of geese and other species. 8 Case Study: Phylogenetic Analysis of Swan Goose-Derived Chinese Breeds 8.1 Background and sampling design Most of the native rare species of Chinese geese originated from Swan goose (Anser cygnoides). Because they have a unique genetic background and their numbers are decreasing, they have high conservation value. To study their evolution, blood samples were collected from six representative goose breeds, namely Lingxiang White (LX), Yan (YE), Yangjiang (YJ), Wuzong (WZ), Xupu (XP), and Baizi (BZ), in this case study. Gender balance was also maintained during sampling (♂:♀ = 1:1). This case study analyzed the mitochondrial cytochrome b (CYTB) gene sequences of these geese and evaluated their genetic diversity, population structure, and historical population changes (Figure 2) (Qi et al., 2024). Figure 2 The six geographic collection points for the endemic endangered geese (Adopted from Qi et al., 2024) Image caption: Images of different goose breeds were captured using a digital camera (Osaka, Japan); LX, Lingxiang White; YE, Yan; YJ, Yangjiang; WZ, Wuzong; XP, Xupu; BZ, Baizi; the irregular black shapes (rectangle, triangle, etc.) in the figure represent the collection locations of the experimental animals, the rectangle in the bottom right corner is a part of Chinese territory (Adopted from Qi et al., 2024) 8.2 Results from mitochondrial and nuclear data comparison Through the analysis of the mitochondrial CYTBgene, researchers discovered a total of 117 loci with variations in these six goose breeds and identified 81 different haplotypes, indicating that they have a high degree of genetic diversity. The haplotype diversity of YJ, YE and WZ is particularly prominent (Hd > 0.9), and there is frequent gene exchange among LX, YJ, YE and WZ (Nm > 15.00), indicating that the genetic relationship among these varieties is relatively close. These six varieties can be divided into six major mitochondrial lineages based on mitochondrial data, reflecting that they have diverse genetic sources. The results of the neutral test (Tajima’s D and Fu’s Fs) and the mismatch distribution showed that the populations of WZ and YJ were relatively stable, and no signs of recent rapid expansion or bottleneck events were found (Qi et al., 2024). The research conducted by Ely et al. (2017) demonstrated that mitochondria are maternally inherited with less gene flow, and usually can more clearly display the population structure. Nuclear DNA markers, due to a greater number of gene flows, exhibit lower genetic differentiation. 8.3 Implications for breeding and conservation Some goose breeds exhibit high mitochondrial diversity and frequent gene exchange, indicating that maintaining genetic ties among breeds is very important for enhancing their adaptability. Qi et al. (2024) found that compared
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