International Journal of Molecular Evolution and Biodiversity, 2025, Vol.15, No.1, 29-39 http://ecoevopublisher.com/index.php/ijmeb 33 relatively low evolutionary pressure or the need to adapt to the environment, mitochondria may become much faster than nuclear DNA, thus embarking on a different “evolutionary path”. 5.2 Case examples in Chinese goose populations Although there is still a lack of direct research on the inconsistency between the mitochondrial and nuclear genomes of Chinese goose species at present, studies on other animals can provide us with some references. Berbel-Filho et al. (2022) discovered a large number of gene infiltration events in Kryptolebias of the genus killifish, causing the types of mitochondria and the lineage of nuclear genes to not match, revealing the hidden genetic diversity and complex evolutionary process behind them. It has also been found in the studies of rotifers and toads that situations such as hybridization and lineage inconsistencies (ILS) can all lead to this genetic inconsistency. In these cases, the study found that the markers of nuclear DNA could reflect the appearance and ecological differences of animals more accurately than those of mitochondria (Papakostas et al., 2016; Firneno et al., 2020). From this, it can be inferred that in China's goose breeds, similar situations may have occurred in the past, such as historical hybridization, rapid formation of goose breeds, or incomplete lineage differentiation, etc. These processes may lead to conflicts in the evolutionary tree, making the true genealogical relationships and the origin of species less clear. 5.3 Implications for species and breed classification The research conducted by Papakostas et al. (2016) and by Campbell et al. (2020) found that mtDNA sometimes fails to accurately reflect the true boundaries between species, which may lead to classification errors or overlook some hidden genetic diversity. It is unlikely to solve these problems solely by mitochondrial data. Data on nuclear genomic information, morphological characteristics, and ecological environment, among others, need to be used together. Only by adopting a more comprehensive phylogenetic approach can genealogical conflicts be better handled and which species are independent be clearly determined (Papakostas et al., 2016; Campbell et al., 2020; Layton et al., 2020). This comprehensive approach is particularly important for geese. It is helpful for clarifying how each variety came about, gaining a deeper understanding of their evolutionary mechanisms, and formulating reasonable conservation and breeding plans. 6 Phylogenetic Methods and Multi-Locus Integration 6.1 Species tree estimation tools Models like MP-EST and ASTRAL, which are based on the “common ancestor theory”, can specifically handle the differences between different gene trees. In the same year, Meiklejohn et al. (2016), Mirarab et al. (2016), and Ottenburghs et al. (2016) found that if a sufficiently accurate gene tree could be obtained, these methods were usually more reliable than the traditional “concatenation” method. Mirarab et al. (2016) and Kimball et al. (2019) demonstrated that there are some other methods, such as Supertree and summary methods (like MRP and MRL), which can combine many small gene trees together, improving efficiency and being suitable for analyzing large-scale genomic data. Phylogenetic analysis strategies based on super-conserved elements (UCEs) and exons have also been successfully applied to complex groups like geese, solving the problem that their evolutionary relationships are difficult to clarify (Meiklejohn et al., 2016; Ottenburghs et al., 2016). 6.2 Comparative evaluation of mitochondrial and nuclear trees The effective population size of mitochondrial DNA is relatively small and often shows relatively obvious signals in the differentiation between species. When it is analyzed together with nuclear DNA, it can enhance the resolution ability of the evolutionary tree (Corl and Ellegren, 2013). However, if only mitochondrial DNA is relied on, the complex evolutionary history may not be clear, especially when the lineages are not completely separated (ILS) or there are hybridization cases, its information may not be sufficient (Corl and Ellegren, 2013; Ottenburghs et al., 2016). In contrast, nuclear DNA, especially genes on sex chromosomes and autosomes, can provide stronger resolution and greater stability when the sample size is sufficient (Corl and Ellegren, 2013). Although the method of combining multiple genes together can receive a high approval rate, it may also mask the inconsistencies among different genes and even increase systematic errors. Adopting the common ancestor model or consensus method can better handle the differences among these gene trees and provide more reliable results in the case of complex evolutionary processes (Mirarab et al., 2016; Farah et al., 2021).
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