International Journal of Molecular Zoology, 2025, Vol.15, No.1, 1-9 http://animalscipublisher.com/index.php/ijmz 3 3 Phylogenetic Reconstruction and Evolutionary Patterns inCapra The phylogenetic past of Capra is one that involves solving gene tree conflict using advanced methods that account for ILS and introgression. These processes cause the reticulate evolutionary patterns observed in Capra, hence the necessity of using comprehensive phylogenomic analysis to untangle its complex evolutionary history. 3.1 Phylogenetic tree construction using multiple methods For the construction of phylogenetic trees for Capra species, scientists prefer to utilize combinations of methods such as maximum likelihood (ML), Bayesian inference, and coalescent methods. These allow for full depiction of the relationships of the species through the consideration of more than a single source of information as well as variability. ML and Bayesian methods can deal with large-scale genomics and also produce large-resolution trees. Coalescent methods come in handy in such cases of ILS cases and gene tree-mismatching scenarios-scenarios common in rapidly evolving lineages (Figure 1) (Morales‐Briones et al., 2020; Meleshko et al., 2021; Wang et al., 2023; Herrig et al., 2024). Figure 1 Phylogenetic tree of Capra(Adopted from Wang et al., 2023) Image caption: The colored circles (A-E) correspond to the evolutionary branches A-E in the phylogenetic tree (Adopted from Wang et al., 2023) 3.2 Gene tree discordance and analysis of incomplete lineage sorting (ILS) Gene tree discordance is a common scenario in systematic genomics inference, primarily induced by factors like incomplete lineage sorting (ILS) and hybridization. In the genus Capra, ILS has the potential to cause divergent genomic regions bearing contradictory phylogenetic signals and making it challenging to reconstruct truthful germline trees. This has been through the development of software such as Phytop to measure and visualize the amount of ILS hybridization to facilitate identification of phylogenetic uncertainty as well as elucidation of the evolutionary history of complicated lineages (Morales‐Briones et al., 2020; Shang et al., 2024). A profound understanding of the impact of ILS is the remedy for addressing gene tree conflict and the improvement of phylogenetic inference accuracy (Hibbins et al., 2020). 3.3 Genome-wide evidence of introgression and historical hybridization Wen et al. (2016) found that historical infiltration and hybridization played a pivotal role in evolutionary history within the genus Capra. Genome-wide phylogenetic comparison reveals that infiltration can lead to the loss of the species' phylogenetic boundary, and the phenomenon also often occurs in oak tree and mosquito clades. On the one hand, they facilitate the accumulation of genetic diversity, and on the other hand, they are a reticular complex
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