Parentage allocation in a complex situation:: A large commercial Atlantic cod (Gadus morhua) mass spawning tank
Parentage allocation in a complex situation:: A large commercial Atlantic cod (Gadus morhua) mass spawning tank
复制标题
DOI：
10.1016/j.aquaculture.2007.08.018
复制
发表时间：
2007-01-01
期刊：
影响因子：
4.5
通讯作者：
Penman, David J.
中科院分区：
文献类型：
--
作者：
Herlin, Marine;Taggart, John B.;Penman, David J.
亲子鉴定作为监测水产养殖业实践影响的一种手段越来越受欢迎。随着这些研究的复杂性增加，基于可能性的分配方法正在脱颖而出，因为至少在理论上，与基于排除的方法相比，它们提供了以更少的筛选开销（更少的位点，更低的成本）进行准确分配的可能性。我们能够探索这一论断通过分析的父母的贡献300大西洋鳕鱼（Gadus morhua）飞从商业大规模产卵池（含99亲鱼）在一天。筛选了5个多态性DNA微卫星位点，并生成了3个不同的数据集：来自自动等位基因调用的"易出错"原始基因型数据;手动校正的数据;以及来自减少数量的位点（4个）的校正数据。亲子关系分析是由三个软件包-PAPA，CERVUS和FAP-这都已在水产养殖环境中使用。PAPA和CERVUS进行基于可能性的分析，而FAP是基于排除的。引人注目的差异分配性能之间的程序和数据集。在不允许错误的情况下，所有三个程序都标记了数据集中的潜在问题，特别是容易出错的“原始”基因型。当使用PAPA（均匀误差率= 0.0001 - 0.02）调用假定的低水平误差时，几乎所有后代都被分配了亲子关系，而与使用的数据集无关。尽管模拟表明这些分配可能是准确的（正确率> 95%），但数据集之间的分配数量（高达18%）不同。FAP给出了更保守的（最大c。78%的任务得到解决）和一致的任务。当只考虑四个位点时，分配的能力显着下降。CERVUS在分配数量方面表现相对较差。在比较是可能的，大多数确定的父母对同意FAP分配。在复杂的大规模产卵池中，仅仅依靠基于可能性的分配来解决亲子关系可能是不合适的。此外，将基因座的数量减少到最小集合（基于可能性预测）可能会适得其反。应更彻底地评估和充分说明分配方法。(c)2007 Elsevier B.V.保留所有权利。
Parentage assignment is becoming increasingly popular as a means of monitoring the effects of aquaculture husbandry practices. As the complexity of such studies increase, likelihood-based methods for assignment are coming to the fore since, theoretically at least, they offer the possibility of accurate assignment with less screening overheads (fewer loci, less cost) compared to exclusion-based methods. We were able to explore this assertion through the analysis of the parental contribution to 300 Atlantic cod (Gadus morhua) fiy produced from a commercial mass spawning tank (containing 99 broodstock) on a single day. Five polymorphic DNA microsatellite loci were screened and three different datasets generated: 'error prone' raw genotypic data from automated allele calling; manually corrected data; and corrected data from a reduced number of loci (four). Parentage analysis was performed by three software packages-PAPA, CERVUS and FAP-which all have been used in aquaculture contexts. PAPA and CERVUS perform likelihood-based analyses, while FAP is exclusion-based. Striking differences in the allocation performance were noted both among programs and among datasets. With no allowance for error all three programs flagged up potential problems within datasets, particularly the error prone 'raw' genotypes. When allowance for a presumed low level of error was invoked using PAPA (uniform error rate = 0.0001-0.02) parentage was assigned for virtually all offspring, irrespective of the dataset used. Despite simulations suggesting that these assignments were likely to be accurate (correctness values >95%) substantial numbers of assignments (up to 18%) differed among the datasets. FAP gave more conservative (maximum of c. 78% of assignments resolved) and consistent assignments. The power of assignment declined significantly when only four loci were considered. CERVUS performed relatively poorly in terms of numbers of assignments made. Where comparisons were possible most of the identified parental-pairs agreed with FAP allocations. Reliance on likelihood-based assignments alone to resolve parentage in complex mass spawning tanks may be inappropriate. Furthermore, reducing the number of loci to a minimal set (based on likelihood predictions) could be counterproductive. Allocation methods should be more thoroughly assessed and fully described. (c) 2007 Elsevier B.V. All rights reserved.