Comparing genome-based estimates of relatedness for use in pedigree-based conservation management

Researchers have long debated which estimator of relatedness best captures the degree of relationship between two individuals. In the genomics era, this debate continues, with relatedness estimates being sensitive to the methods used to generate markers, marker quality, and levels of diversity in sampled individuals. Here, we compare six commonly used genome-based relatedness estimators (kinship genetic distance (KGD), Wang Maximum Likelihood (TrioML), Queller and Goodnight (Rxy), Kinship INference for Genome-wide association studies (KING-robust), and Pairwise Relatedness (RAB), allele-sharing co-ancestry (AS)) across five species bred in captivity–including three birds and two mammals–with varying degrees of reliable pedigree data, using reduced-representation and whole genome resequencing data. Genome-based relatedness estimates varied widely across estimators, sequencing methods, and species, yet the most consistent results for known first order relationships were found using Rxy, R...长期以来，学界始终围绕哪一种亲缘关系估计器能够最优刻画两个个体间的亲缘程度展开争论。步入基因组学时代后，这一争论仍未停歇：亲缘关系估计结果对标记生成方法、标记质量以及采样个体的多样性水平均具有高度敏感性。本研究以5种人工繁育物种（含3种鸟类、2种哺乳类）为研究对象，这些物种的系谱数据可靠程度各不相同，同时采用简化代表性测序与全基因组重测序数据，对6种常用的基于基因组的亲缘关系估计器进行比较：亲缘遗传距离（kinship genetic distance, KGD）、Wang最大似然估计器（Wang Maximum Likelihood, TrioML）、Queller与Goodnight估计量（Queller and Goodnight, Rxy）、全基因组关联分析亲缘推断稳健法（Kinship INference for Genome-wide association studies, KING-robust）、成对亲缘关系估计量（Pairwise Relatedness, RAB）以及等位基因共享共祖率（allele-sharing co-ancestry, AS）。基于基因组的亲缘关系估计值在不同估计器、测序方法与物种间差异显著；但针对已知的一级亲缘关系，Rxy、R……得到了最为一致的分析结果。