Department of Ecology, Evolution and Environmental Biology, Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY, USA.
Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zürich, Switzerland.
Mol Ecol Resour. 2022 Nov;22(8):2981-2993. doi: 10.1111/1755-0998.13680. Epub 2022 Jul 22.
Genealogical relationships are fundamental components of genetic studies. However, it is often challenging to infer correct and complete pedigrees even when genome-wide information is available. For example, inbreeding can obscure genetic differences between individuals, making it difficult to even distinguish first-degree relatives such as parent-offspring from full siblings. Similarly, genotyping errors can interfere with the detection of genetic similarity between parents and their offspring. Inbreeding is common in natural, domesticated, and experimental populations and genotyping of these populations often has more errors than in human data sets, so efficient methods for building pedigrees under these conditions are necessary. Here, we present a new method for parent-offspring inference in inbred pedigrees called specific parent-offspring relationship estimation (spore). spore is vastly superior to existing pedigree-inference methods at detecting parent-offspring relationships, in particular when inbreeding is high or in the presence of genotyping errors, or both. spore therefore fills an important void in the arsenal of pedigree inference tools.
系谱关系是遗传研究的基本组成部分。然而，即使有全基因组信息可用，推断正确和完整的系谱也常常具有挑战性。例如，近亲繁殖会使个体之间的遗传差异变得模糊，甚至难以区分亲子关系（例如父母与子女）和全同胞关系。同样，基因分型错误会干扰父母与其后代之间遗传相似性的检测。近亲繁殖在自然、驯化和实验种群中很常见，这些种群的基因分型通常比人类数据集有更多的错误，因此在这些条件下构建系谱的有效方法是必要的。在这里，我们提出了一种称为特定亲子关系估计（spore）的新方法，用于近亲系谱中的亲子推断。spore 在检测亲子关系方面明显优于现有的系谱推断方法，尤其是在近亲繁殖程度高或存在基因分型错误或两者兼有的情况下。因此，spore 填补了系谱推断工具库中的一个重要空白。
