International Journal of Molecular Evolution and Biodiversity, 2025, Vol.15, No.1, 29-39 http://ecoevopublisher.com/index.php/ijmeb 32 Figure 1 Selective signals for the white plumage phenotype of geese (Adopted from Jing et al., 2022) Image caption: a: Manhattan plot of zFst between white and gray geese; b: Manhattan plot of zHp in white geese, with the positions matching zFst; the gray dashed line represents the top 1% cutoff; c: the plot of the haplotype structure of variants around the EDNRB2 and POLR1D genes in all domestic geese and wild populations (the genera Anser and Cygnus in the Anatidae family); major and minor alleles in GFW are indicated by beige and light blue, respectively; the red box represents the unique haplotypes of white geese; the black arrow indicates the position (15 764 637 bp) of the candidate causal 14-bp insertion for the white geese; the red and black rectangles in the bottom box represent the UTRs and CDSs, respectively. d Haplotype network based on 285 SNPs and Indels from the EDNRB2 gene (15 763 328 bp) to POLR1D gene (15 779 122 bp) on chromosome 15; each circle represents a haplotype, and the size of the circle is proportional to the haplotype frequency. The line width and length represent the difference between haplotypes; GFW: Guangfeng white goose, HYG: Huoyan goose, LHW: Lianhua white goose, LXW: Lingxian white goose, MBW: Mingbei white goose, FCG: Fengcheng gray goose, STG: Shitou goose, WZG: Wuzong goose, XGG: Xingguo gray goose, LDG: Landaise goose, ACy: Anser cygnoides, CCo: Cygnus columbianus (Adopted from Jing et al., 2022) 5 Mitonuclear Discordance in Phylogenetic Reconstruction 5.1 Mechanisms of phylogenetic incongruence The research conducted by Li and Lu (2024) demonstrated that when using mitochondrial DNA (mtDNA) and nuclear DNA (nDNA) to draw evolutionary trees, the two results sometimes differ. This situation is known as “mitonuclear discordance”. There are several reasons for this inconsistency. One is “Genealogical Inconsistencies” (ILS). Some gene types left by ancestors are still retained in different populations, which makes the drawn gene trees look inconsistent. Firneno et al. (2020) and DeRaad et al. (2023) hold that this situation is more common in groups where species evolve rapidly, as the time when mitochondria and nuclear DNA return to a common ancestor may be different. Another situation is “gene infiltration”, that is, when different species hybridization occurs and gene fragments are transferred there, “mitochondrial capture” - it is possible when the mitochondrial DNA of one species is completely replaced by another, but their nuclear DNA is still different (Layton et al., 2020; Mao and Rossiter, 2020; Berbel-Filho et al., 2022). Quattrini et al. (2023) and Zhang et al. (2024) demonstrated that different selection pressures can also affect the evolutionary speed of mitochondria. Sometimes, due to
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