International Journal of Molecular Evolution and Biodiversity, 2025, Vol.15, No.1, 29-39 http://ecoevopublisher.com/index.php/ijmeb 34 6.3 Toward a consensus phylogeny for domestic geese Ottenburghs et al. ’s research on True Geese (Anserini) in 2016 found that combining whole-genome data and using the “connection method” and the “common ancestor model” to build a consensus tree can well solve some controversial evolutionary relationships and also more clearly determine the time point of species differentiation. The evolutionary trees drawn by these two methods are very consistent, both supporting the division of True Geese into two main lineages, Anser and Branta, and each genus has more detailed branch structures. The consensus tree also indicates that there are many rapid new species formation processes and hybridization events within the genus Anser, all of which have a significant impact on their evolutionary relationships. The research of Ottenburghs et al. (2016) further indicates that it is very important to integrate multiple gene loci when constructing a phylogenetic tree. Corl and Ellegren (2013), as well as Ottenburghs et al. (2016), discovered that if data from mitochondria and nuclear DNA could be combined and advanced establishment methods were adopted, the complex evolutionary history between domestic geese and their close relatives could be understood more effectively. 7 Functional Evolution in Mitochondrial Genes 7.1 Selection in oxidative phosphorylation genes In mitochondria, the genes responsible for the oxidative phosphorylation (OXPHOS) process are important for cellular energy production and are usually highly functionally limited. However, these genes also show signs of adaptive evolution, especially to meet the metabolic needs of different species. Some amino acid changes in cytochrome b and other Oxphos-related genes may be related to specific metabolic or environmental stresses, such as low-energy diets, large-sized animals, or situations that require special oxygen regulation, such as diving, flying, and high altitudes. These changes are often concentrated in some regions that are particularly important for function, such as the cyclic structural region of NADH dehydrogenase, or the locations where mitochondria and nuclear coding subunits interact in cytochrome c oxidase, indicating that these genes may not only undergo structural changes but also functionally adapt to different selection pressures. The two subunits ATP8 and ATP6 show high adaptive changes, indicating that they play an important role in the assembly and function of the OXPHOS complex (Da Fonseca et al., 2008). 7.2 Mitonuclear co-evolution and compensation hypotheses Mitochondrial genes and nuclear genes need to cooperate together in the OXPHOS complex of mitochondria to ensure the efficient progress of cellular respiration, so they must “co-evolve”. The OXPHOS proteins encoded by mitochondria and the nucleus are highly correlated in the rate of evolution, which supports the claim of “mitochondrial-nuclear gene co-evolution”. Changes in one genome are usually adjusted accordingly by the other genome to maintain normal functions (Sunnucks et al., 2017; Piccinini et al., 2021; Weaver et al., 2022). Regarding the hypothesis of “nuclear compensation” - that is, nuclear genes can remedy harmful mutations in mitochondria - there is currently not much direct evidence. Piccinini et al. (2021) and Weaver et al. (2022) demonstrated that some studies did indeed find an increase in the dN/dS ratio of the nuclear OXPHOS gene, but no obvious signals of compensatory positive selection were generally observed at specific locations, and the time distribution of amino acid substitution did not consistently indicate that nuclear compensation played a key role. Researchers believe that “reciprocal coevolution” or “division of labor and variation after gene replication” may better explain these evolutionary patterns (Havird and McConie, 2019; Piccinini et al., 2021). Sunnucks et al. (2017) and Morales et al. (2018) argued that some structural characteristics of the genome, such as the tight aggregation of mitochondrial functional-related genes in certain regions, might also promote this mutually adaptive evolution. 7.3 Adaptive signatures in wild vs. domesticated populations Sunnucks et al. (2017) found in the process of studying the adaptation of bar-headed geese to the high-altitude environment that both mitochondrial genes and nuclear OXPHOS genes showed obvious selection signals when facing environmental stress. Population differentiation and local adaptation in birds change along with the mitochondrial genome and the nuclear gene clusters that control mitochondrial function. Morales et al. (2018) found that in populations living under different climatic conditions, the phenomenon of “selective sweeping” often
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