从SNP数据估计当代有效人口规模,同时考虑交配结构
Enrique Santiago1, Armando Caballero2, Carlos Köpke3
1Departamento de Biología Funcional, Facultad de Biología, Universidad de Oviedo, Oviedo, Spain.
Molecular ecology resources
|November 8, 2023
概括
一种新的方法估计有效种群大小 (Ne) 使用链接不平衡 (LD) 没有SNP位置. 这种方法可以解释全,改善了各种物种和交配系统中的Ne估计.
科学领域:
- 人口遗传学 人口遗传学
- 生物信息学是一种生物信息学.
- 计算生物学 计算生物学
背景情况:
- 估计当代有效人口规模 (Ne) 对于理解人口动态至关重要.
- 传统方法通常需要遗传标记物位置数据,限制在非模型物种中的应用.
- 链接不平衡 (LD) 是一个有价值的遗传标记,用于推断人口历史和规模.
研究的目的:
- 开发一种新的方法来估计当代有效种群大小 (Ne) 使用基于SNP的LD而不需要标记物位置数据.
- 扩展LD理论,将全对各种交配系统的Ne估计的影响纳入其中.
- 为Ne估计提供准确的置信区间,即使在具有挑战性的场景中.
主要方法:
- 开发了一种新的方法,在没有位置信息的情况下,在单核酸多态 (SNPs) 之间估计来自LD的Ne.
- 扩展了LD理论,包括全兄弟姐妹的贡献,适用于单性,多妻性和多妻性物种.
- 利用一个小型人工神经网络,在超过10^5次的模拟中进行训练,以预测Ne估计的置信区间.
主要成果:
- 这种新方法准确地估计了没有SNP位置的LD的Ne,适合非模型生物.
- 该方法成功地结合了全sib效应,增强了复杂的交配系统和家庭结构中的Ne估计.
- 实施的软件 (currentNe) 提供了比重新采样方法更一致的置信区间,即使采用大种群或小样本大小.
结论:
- 已经建立了一种强大而通用的方法来估计当代有效人口大小 (Ne).
- 开发的方法和软件 (currentNe) 为人口遗传研究提供了显著的优势,特别是在非模型物种中.
- 这种方法提高了Ne估计的可靠性及其相关的置信区间在不同的生物环境.
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