Division of Genetics and Physiology, Department of Biology, University of Turku, Turku, Finland.
BMC Evol Biol. 2014 Mar 31;14(1):68. doi: 10.1186/1471-2148-14-68.
Pedigree reconstruction using genetic analysis provides a useful means to estimate fundamental population biology parameters relating to population demography, trait heritability and individual fitness when combined with other sources of data. However, there remain limitations to pedigree reconstruction in wild populations, particularly in systems where parent-offspring relationships cannot be directly observed, there is incomplete sampling of individuals, or molecular parentage inference relies on low quality DNA from archived material. While much can still be inferred from incomplete or sparse pedigrees, it is crucial to evaluate the quality and power of available genetic information a priori to testing specific biological hypotheses. Here, we used microsatellite markers to reconstruct a multi-generation pedigree of wild Atlantic salmon (Salmo salar L.) using archived scale samples collected with a total trapping system within a river over a 10 year period. Using a simulation-based approach, we determined the optimal microsatellite marker number for accurate parentage assignment, and evaluated the power of the resulting partial pedigree to investigate important evolutionary and quantitative genetic characteristics of salmon in the system.
We show that at least 20 microsatellites (ave. 12 alleles/locus) are required to maximise parentage assignment and to improve the power to estimate reproductive success and heritability in this study system. We also show that 1.5 fold differences can be detected between groups simulated to have differing reproductive success, and that it is possible to detect moderate heritability values for continuous traits (h2 ~ 0.40) with more than 80% power when using 28 moderately to highly polymorphic markers.
The methodologies and work flow described provide a robust approach for evaluating archived samples for pedigree-based research, even where only a proportion of the total population is sampled. The results demonstrate the feasibility of pedigree-based studies to address challenging ecological and evolutionary questions in free-living populations, where genealogies can be traced only using molecular tools, and that significant increases in pedigree assignment power can be achieved by using higher numbers of markers.
通过遗传分析进行系谱重建，结合其他数据源，为估计与人口统计学、性状遗传力和个体适合度相关的基本群体生物学参数提供了一种有用的方法。然而，在野生种群中，系谱重建仍然存在一些局限性，特别是在无法直接观察亲代-子代关系、个体采样不完全或分子亲子关系推断依赖于存档材料中低质量 DNA 的情况下。尽管从不完整或稀疏的系谱中仍然可以推断出很多信息，但在测试特定的生物学假设之前，对可用遗传信息的质量和能力进行预先评估是至关重要的。在这里，我们使用微卫星标记，通过在一条河流中使用总捕获系统在 10 年内收集的存档鳞片样本，重建了野生大西洋鲑（Salmo salar L.）的多代系谱。通过基于模拟的方法，我们确定了准确亲子关系分配的最佳微卫星标记数量，并评估了由此产生的部分系谱调查系统中鲑鱼重要进化和数量遗传特征的能力。
我们表明，至少需要 20 个微卫星（平均 12 个等位基因/座）才能最大限度地提高亲子关系分配，并提高在该研究系统中估计繁殖成功率和遗传力的能力。我们还表明，模拟繁殖成功率不同的群体之间可以检测到 1.5 倍的差异，并且使用 28 个中度到高度多态性标记，对于连续性状（h2~0.40），可以以 80%以上的概率检测到中等遗传力值。
所描述的方法和工作流程为评估基于系谱的研究的存档样本提供了一种稳健的方法，即使仅对总人群的一部分进行采样也是如此。结果表明，即使在只能使用分子工具追踪系谱的自由生活种群中，基于系谱的研究也可以解决具有挑战性的生态和进化问题，并且通过使用更多数量的标记可以显著提高系谱分配能力。
