Can nuclear aquatic environmental DNA be a genetic marker for the accurate estimation of species abundance?
Can nuclear aquatic environmental DNA be a genetic marker for the accurate estimation of species abundance?
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核水生环境DNA能否成为准确估计物种丰度的遗传标记？
DOI：
10.1007/s00114-022-01808-7
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发表时间：
2022
期刊：
影响因子：
--
通讯作者：
Yamanaka Hiroki
中科院分区：
文献类型：
--
作者：
Jo Toshiaki S.;Tsuri Kenji;Yamanaka Hiroki
环境DNA （Environmental DNA, eDNA）分析是一种灵敏、有效地监测物种分布和丰度的有前途的工具。传统的eDNA分析主要针对线粒体DNA （mtDNA）片段，因为它们在细胞中含量丰富；然而，定量可能因细胞类型和生理而异。相反，最近的一些eDNA研究针对水中的多拷贝核DNA （nuDNA）片段，如核糖体RNA基因，并报道了比线粒体eDNA （mt-eDNA）更高的可检测性和更快的降解。这些特性表明，核eDNA （nu-eDNA）可能有助于准确估计相对于mt-eDNA的物种丰度，但目前尚不清楚。在本研究中，我们整理了前人的研究成果，通过比较线性回归的ther2值，重新分析了mt-和nu-eDNA浓度与物种丰度之间的关系。然后，我们用斑马鱼（Danio rerio）进行了一个水族馆实验，比较了遗传区域之间的关系，包括单拷贝nuDNA。在这些数据集中，我们发现多拷贝nu-eDNA与物种丰度之间的关系比mt-eDNA更准确，尽管在加权平均ther2值时差异不显著。此外，我们比较了斑马鱼不同遗传区域eDNA的衰变速率常数，发现pH为7时，多拷贝nu-eDNA的降解速度比mt-eDNA快，这意味着多拷贝nu-eDNA在田间的快速更替。虽然需要进一步的实证研究来支持我们的研究结果，但本研究为通过eDNA分析提高物种丰度估计的准确性提供了基础。
Environmental DNA (eDNA) analysis is a promising tool for the sensitive and effective monitoring of species distribution and abundance. Traditional eDNA analysis has targeted mitochondrial DNA (mtDNA) fragments due to their abundance in cells; however, the quantification may vary depending on cell type and physiology. Conversely, some recent eDNA studies have targeted multi-copy nuclear DNA (nuDNA) fragments, such as ribosomal RNA genes, in water, and reported a higher detectability and more rapid degradation than mitochondrial eDNA (mt-eDNA). These properties suggest that nuclear eDNA (nu-eDNA) may be useful for the accurate estimation of species abundance relative to mt-eDNA, but which remains unclear. In this study, we compiled previous studies and re-analyzed the relationships between mt- and nu-eDNA concentration and species abundance by comparing theR2values of the linear regression. We then performed an aquarium experiment using zebrafish (Danio rerio) to compare the relationships across genetic regions, including single-copy nuDNA. We found more accurate relationships between multi-copy nu-eDNA and species abundance than mt-eDNA in these datasets, although the difference was not significant upon weighted-averaging theR2values. Moreover, we compared the decay rate constants of zebrafish eDNA across genetic regions and found that multi-copy nu-eDNA degraded faster than mt-eDNA under pH 7, implying a quick turnover of multi-copy nu-eDNA in the field. Although further empirical studies of nu-eDNA applications are necessary to support our findings, this study provides the groundwork for improving the estimation accuracy of species abundance via eDNA analysis.
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发表时间：
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