对基因家族进化对副本数血流病的影响
Qiuyi Li1,2, Yao-Ban Chan1, Nicolas Galtier3
1School of Mathematics and Statistics/Melbourne Integrative Genomics, The University of Melbourne, Melbourne 3010, Australia.
基因家族进化是复杂的,因为基因重复,损失和不完整的血统分类 (ILS). 拷贝数组分离 (CNH) 产生于它们的相互作用,显著影响基因拷贝数量和重复率估计.
科学领域:
- 进化生物学是进化的生物学.
- 基因组学就是基因组学.
- 计算生物学是一种计算生物学.
背景情况:
- 基因家族的进化是由基因重复,水平基因转移,基因丢失和不完整的血统分类 (ILS) 所塑造的.
- 由于这些复杂的进化过程,基因树和物种树之间的拓差异很常见.
- 现有的模型很难有效地统一基因级事件和ILS.
研究的目的:
- 扩展赖特-费舍尔过程以模拟多个物种的基因重复和损失.
- 调查复制数半失质 (CNH) 现象及其概率.
- 为了比较 CNH (MLMSC) 与不包括 (DLCoal) 的模型的性能,在近似扩展的赖特-费舍尔过程中.
主要方法:
- 扩展了赖特-费舍尔过程,将基因重复和损失纳入多个物种环境中.
- 开发并比较了两个统一的模型:MLMSC (建模CNH) 和DLCoal (不建模CNH).
- 在两种模型下生成可比的基因树,用于比较分析和物种树推断.
主要成果:
- 扩展的赖特-费舍尔过程可以导致CNH的显著概率.
- 与没有CNH的模型相比,CNH显著减少了基因拷贝的数量.
- 当不考虑CNH时,估计基因复制率的传统方法是不准确的.
- 在模拟中忽略CNH时,物种树推断方法 (ASTRAL,ASTRAL-Pro) 可能会高估准确性.
结论:
- CNH是基因家族进化的关键因素,必须纳入进化模型.
- 没有考虑CNH导致基因复制率的不准确估计.
- 由于CNH无意识模拟,物种树推断方法的准确性可能被高估.
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