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维基百科,自由的百科全书

基因组学基础

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  • k-mer方法在生信中的应用:Moeckel et al., 2024 [1]

基因组略读

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检测杂交

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  • 从基因组学角度理解杂交和种化:Payseur and Rieseberg, 2016
    • “我们建议谨慎将对整个基因组variation的总结性分析结果解读为differential基因流。We argue that converting genomic patterns into useful inferences about hybridization will ultimately require models and methods that directly incorporate key ingredients of speciation, including the dynamic nature of gene flow, selection acting in hybrid populations and recombination rate variation.”
    • “表现出不寻常规律的基因位点常与生殖隔离相关。这些位点通常散布在基因组各处,且可能在性染色体遗传重组较少的区域富集。”
  • 比较几种基于基因组数据的常用杂交检验方法:Kong and Kubatko, 2021[2]
    • "HyDe和D-statistic在大部分情况下(ILS较高的话除外)都可以有效地检测杂交,但D-stat的假发现率较高"
    • "HyDe所预测的γ(i.e. inheritance parameter; quantifies the genomic contributions of the parents to the hybrid)十分robust且准确,而structure和ADMIXTURE尤其在parental contribution不对等(i.e.γ接近于0时)时无法识别杂交。"
    • "使用structure得出的后验分布常呈多峰状,致使难以解读。"
  • 系统发生学中用STRUCTURE法检验杂交的注意事项:Pang and Zhang., 2024 [3]
    • "在基因混合(admixture)事件距今时间非常近的情况下,STRUCTURE可以较好地识别杂交及其parental donors。然而,对于杂交时间较久远,或是ghost lineage参与了基因流的情况,STRUCTURE通常无法检测出admixture信号。"
    • "若是父母在实际的杂交种化事件中对子代的贡献不对等(How does this happen??),STRUCTURE分析结果则会将这种不对等进一步夸大化,尤其是admixture事件时间较久远的情况下。"

參考

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  1. ^ Moeckel, Camille; Mareboina, Manvita; Konnaris, Maxwell A.; Chan, Candace S.Y.; Mouratidis, Ioannis; Montgomery, Austin; Chantzi, Nikol; Pavlopoulos, Georgios A.; Georgakopoulos-Soares, Ilias. A survey of k-mer methods and applications in bioinformatics. Computational and Structural Biotechnology Journal. 2024-12, 23: 2289–2303. doi:10.1016/j.csbj.2024.05.025. 
  2. ^ Kong, Sungsik; Kubatko, Laura S. Comparative Performance of Popular Methods for Hybrid Detection using Genomic Data. Systematic Biology. 2021-09-01, 70 (5): 891–907. doi:https://doi.org/10.1093/sysbio/syaa092 请检查|doi=值 (帮助). 
  3. ^ Xiao-Xu Pang; Da-Yong Zhang. A Cautionary Note on Using STRUCTURE to Detect Hybridization in a Phylogenetic Context. 2024-02-08 [2025-01-21]. doi:10.1101/2024.02.06.579057.