Valid estimates of individual inbreeding coefficients from marker-based pedigrees are not feasible in wild populations with low allelic diversity
Valid estimates of individual inbreeding coefficients from marker-based pedigrees are not feasible in wild populations with low allelic diversity
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DOI：
10.1007/s10592-015-0709-1
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发表时间：
2015-08-01
影响因子：
2.2
通讯作者：
Allendorf, Fred W.
中科院分区：
文献类型：
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作者：
Taylor, Helen R.;Kardos, Marty D.;Allendorf, Fred W.
系谱经常被推荐用于估计近交系数（F（PED）），但由于野生种群中缺少行为数据而容易出错。遗传标记为基础的系谱已被建议作为一种补救措施，这个问题，但其准确性取决于数量和多态性的基因座，以及人口抽样的完整性。我们使用模拟来研究如何标记为基础的系谱的准确性随基因座和采样制度的数量变化时，等位基因多样性低（2.2-4等位基因每个基因座的创始人），往往是在受威胁的物种。我们还研究了系谱误差对F（PED）有效性的影响，F（PED）是从基于标记的系谱中估计的。我们的研究结果表明，准确的亲子鉴定是唯一可行的，如果基因型可用于所有的个人，曾经存在于人口中，准确性并没有提高过去的40个位点。基于标记的家系错误导致F（PED）低估高达27%，F（PED）方差高估高达182%。至少需要80%的系谱准确性来产生F（PED）的无偏估计，这仍然是高度不精确的。鉴于所需的取样程度，目前仅根据微卫星数据来衡量濒危物种野生种群的近亲繁殖是不可行的。资源可以更好地用于开发更强大的遗传工具（全基因组测序和大SNP面板），以促进在没有系谱的情况下直接估计近交系数。如果这是不可能的，将需要长期监测项目，通过结合行为和遗传数据准确估计近亲繁殖系数。
Pedigrees are frequently recommended for estimating inbreeding coefficients (F (PED) ), but are error-prone due to missing behavioural data in wild populations. Genetic marker-based pedigrees have been suggested as a remedy to this problem, but their accuracy depends on the number and polymorphism of loci available, and the completeness of population sampling. We used simulations to examine how accuracy of marker-based pedigrees varies with number of loci and sampling regime when allelic diversity is low (2.2-4 alleles per locus in founders), as is often the case in threatened species. We also examined the impact of pedigree errors on the validity of F (PED) estimated from marker-based pedigrees. Our results indicate that accurate parentage assignments are only feasible if genotypes are available for all individuals that ever existed in the population, and that accuracy does not improve past 40 loci. Errors in marker-based pedigrees resulted in underestimation of F (PED) by up to 27 % and overestimation of the variance in F (PED) by up to 182 %. At least 80 % pedigree accuracy was required to produce unbiased estimates of F (PED) , which were still highly imprecise. Given the degree of sampling required, it is not currently feasible to measure inbreeding in wild populations of threatened species with a pedigree based solely on microsatellite data. Resources may be better directed towards developing more robust genetic tools (whole genome sequencing and large SNP panels) to facilitate direct estimation of inbreeding coefficients without a pedigree. Where this is not possible, long-term monitoring projects will be required to accurately estimate inbreeding coefficients via a combination of behavioural and genetic data.