A simulation study of sample size for DNA barcoding.
A simulation study of sample size for DNA barcoding.
复制标题
DNA条形码样本量的模拟研究
DOI：
10.1002/ece3.1846
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发表时间：
2015-12
影响因子：
2.6
通讯作者：
Zhu C
中科院分区：
文献类型：
--
作者：
Luo A;Lan H;Ling C;Zhang A;Shi L;Ho SY;Zhu C
摘要对于某些生物类群，DNA条形码可以在分类学、进化生物学和生物多样性评价中提供有用的工具。然而，DNA条形码的功效取决于每个物种的采样程度，因为需要足够大的样本量来提供对遗传多态性的可靠估计和用于界定物种。我们使用模拟方法来研究样本量对与DNA条形码相关的遗传多态性的四个估计量的影响：错配分布，核苷酸多样性，单倍型数量和最大成对距离。我们的结果表明，来自≥20个个体的子样本的失配分布通常与完整数据集的失配分布非常相似。来自≥20个个体的子样本的核苷酸多样性估计值倾向于在完整数据集的周围呈钟形，而来自较小子样本的估计值则不是。正如预期的那样，更大的采样通常会导致单倍型数量的增加。我们还发现，≥20个个体的子样本可以很好地估计整个数据集的最大成对距离，而较小的子样本则与低估的高概率相关。总的来说，我们的研究证实了较大样本有利于DNA条形码有效性的预期，并建议每个群体在实践中需要至少20个个体的样本量。
Abstract For some groups of organisms, DNA barcoding can provide a useful tool in taxonomy, evolutionary biology, and biodiversity assessment. However, the efficacy of DNA barcoding depends on the degree of sampling per species, because a large enough sample size is needed to provide a reliable estimate of genetic polymorphism and for delimiting species. We used a simulation approach to examine the effects of sample size on four estimators of genetic polymorphism related to DNA barcoding: mismatch distribution, nucleotide diversity, the number of haplotypes, and maximum pairwise distance. Our results showed that mismatch distributions derived from subsamples of ≥20 individuals usually bore a close resemblance to that of the full dataset. Estimates of nucleotide diversity from subsamples of ≥20 individuals tended to be bell‐shaped around that of the full dataset, whereas estimates from smaller subsamples were not. As expected, greater sampling generally led to an increase in the number of haplotypes. We also found that subsamples of ≥20 individuals allowed a good estimate of the maximum pairwise distance of the full dataset, while smaller ones were associated with a high probability of underestimation. Overall, our study confirms the expectation that larger samples are beneficial for the efficacy of DNA barcoding and suggests that a minimum sample size of 20 individuals is needed in practice for each population.