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Pedigree reconstruction and distant pairwise relatedness estimation from genome sequence data: A demonstration in a population of rhesus macaques (Macaca mulatta)
Molecular Ecology Resources ( IF 7.7 ) Pub Date : 2021-01-01 , DOI: 10.1111/1755-0998.13317
Lauren E Petty 1 , Kathrine Phillippi-Falkenstein 2 , H Michael Kubisch 2 , Muthuswamy Raveendran 3 , R Alan Harris 3 , Eric J Vallender 2, 4 , Chad D Huff 5 , Rudolf P Bohm 2 , Jeffrey Rogers 3 , Jennifer E Below 1
Affiliation  

A primary challenge in the analysis of free‐ranging animal populations is the accurate estimation of relatedness among individuals. Many aspects of population analysis rely on knowledge of relatedness patterns, including socioecology, demography, heritability and gene mapping analyses, wildlife conservation and the management of breeding colonies. Methods for determining relatedness using genome‐wide data have improved our ability to determine kinship and reconstruct pedigrees in humans. However, methods for reconstructing complex pedigree structures and estimating distant relatedness (beyond third‐degree) have not been widely applied to other species. We sequenced the genomes of 150 male rhesus macaques from the Tulane National Primate Research Center colony to estimate pairwise relatedness, reconstruct closely related pedigrees, estimate more distant relationships and augment colony records. Methods for determining relatedness developed for human genetic data were applied and evaluated in the analysis of nonhuman primates, including identity‐by‐descent‐based methods for pedigree reconstruction and shared segment‐based inference of more distant relatedness. We compared the genotype‐based pedigrees and estimated relationships to available colony pedigree records and found high concordance (95.5% agreement) between expected and identified relationships for close relatives. In addition, we detected distant relationships not captured in colony records, including some as distant as twelfth‐degree. Furthermore, while deep sequence coverage is preferable, we show that this approach can also provide valuable information when only low‐coverage (5×) sequence data is available. Our findings demonstrate the value of these methods for determination of relatedness in various animal populations, with diverse applications to conservation biology, evolutionary and ecological research and biomedical studies.

中文翻译:

基于基因组序列数据的谱系重建和远距离成对相关性估计:恒河猴(Macaca mulatta)种群的示范

分析自由放养动物种群的一个主要挑战是准确估计个体之间的相关性。人口分析的许多方面都依赖于相关性模式的知识,包括社会生态学、人口学、遗传力和基因图分析、野生动物保护和繁殖群的管理。使用全基因组数据确定相关性的方法提高了我们确定人类亲属关系和重建谱系的能力。然而,重建复杂谱系结构和估计远亲(超过三度)的方法尚未广泛应用于其他物种。我们对来自杜兰国家灵长类动物研究中心的 150 只雄性恒河猴的基因组进行了测序,以估计成对相关性,重建密切相关的谱系,估计更远的关系并增加殖民地记录。为人类遗传数据开发的确定相关性的方法在非人类灵长类动物的分析中得到应用和评估,包括用于谱系重建的基于身份的血统方法和基于共享片段的更远亲缘关系的推断。我们将基于基因型的谱系和估计的关系与可用的菌落谱系记录进行比较,发现近亲的预期关系和确定的关系之间具有高度的一致性(95.5% 的一致性)。此外,我们还发现了菌落记录中没有记录到的远距离关系,包括一些远至 12 度的关系。此外,虽然深度序列覆盖更可取,但我们表明,当只有低覆盖 (5×) 序列数据可用时,这种方法也可以提供有价值的信息。
更新日期:2021-01-01
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