International Journal of Molecular Evolution and Biodiversity, 2025, Vol.15, No.1, 29-39 http://ecoevopublisher.com/index.php/ijmeb 36 with European goose breeds, the Wright Fixed Index (Fst) of native Chinese geese is relatively lower, which may indicate that their adaptability is weaker and they are more vulnerable to environmental changes or reduced genetic diversity. It is extremely urgent to protect the genetic diversity of goose breeds. Scientific conservation strategies need to be formulated, not only to preserve their genetic resources but also to design targeted breeding plans to enhance their survival ability and adaptability to the environment. Conservation efforts should also make full use of genetic differences within and between populations to better support the long-term development and sustainable utilization of precious goose breeds (Qi et al., 2024). 9 Challenges and Future Directions 9.1 Sampling gaps and geographic biases The true relationships among some species have not been fully clarified due to insufficient and broad sampling. To determine the important time points in the evolutionary process, more types of data are needed, especially the mitochondrial whole-genome data of birds (including geese). The geographical distribution of sampling is not balanced enough. The goose populations in some areas are insufficiently representative. This geographical deviation may mask their true genetic diversity and even miss the signals of gene infiltration (Jing et al., 2022). 9.2 Misleading signals from single-locus studies If the research relies only on one genetic locus, especially only on mitochondrial DNA, it is very likely to be disturbed by factors such as incomplete lineage differentiation, hybridization between species, or gene infiltration. The research conducted by Ottenburghs et al. (2017), DeRaad et al. (2023) and Quattrini et al. (2023) indicates that these circumstances may lead to misleading results for phylogenetic analysis. The kinship among different species of the genus Anser inferred solely from mitochondrial DNA may not reflect their true evolutionary history. This is because during the rapid differentiation of species, coupled with the fact that ancestors already had multiple genetic types, the results can easily become difficult to explain. The situation of "inconsistency between mitochondrial DNA and nuclear DNA evolutionary trees" is very common. This “line-nuclear divergence” is usually caused by the simultaneous occurrence of incomplete lineage separation and gene exchange (DeRaad et al., 2023; Quattrini et al., 2023). 9.3 Data integration and computational demands In order to reconstruct the evolutionary relationships of species more accurately, it is necessary to use the nuclear DNA and mitochondrial data of the entire genome simultaneously, but this approach also brings many computational and analytical difficulties. Compared with mitochondrial genes, nuclear DNA has a lower substitution saturation rate and stronger phylogenetic signals, and usually performs better when studying the deep-level differentiation among species. But the problem is that analyzing such large datasets containing a large number of gene loci requires more complex statistical methods and a lot of computing resources. These challenges are more obvious when hybridization, gene infiltration, and differences between different gene trees need to be considered (Ottenburghs et al., 2017; DeRaad et al., 2023; Quattrini et al., 2023). 9.4 Future directions in goose phylogenetics Ottenburghs et al. (2017) and Jing et al. (2022) hold that future research should focus on conducting more comprehensive sampling throughout the entire distribution range of geese, combining data from both nuclear and mitochondrial genomes, in order to better understand their evolutionary history. Nowadays, there are some new statistical tools, such as hybrid network analysis and D-statistic, which are helpful for distinguishing the effects of hybridization and incomplete lineage separation (Ottenburghs et al., 2017; DeRaad et al., 2023), this is very useful for interpreting the complex signals in genetic data. Jing et al. (2022) indicated that with the development of chromosome-level genome assembly technology and the advancement of population genomics research, it will help to gain a deeper understanding of the genetic diversity, adaptive evolution, and the influence mechanism of artificial selection of domestic geese and wild geese. Acknowledgments The authors thank for the modification suggestions from two anonymous peer reviewers on the manuscript of this study.
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