Fine‐tuning the performance of abundance estimation based on environmental <scp>DNA</scp> ( <scp>eDNA</scp> ) focusing on <scp>eDNA</scp> particle size and marker length
Fine‐tuning the performance of abundance estimation based on environmental <scp>DNA</scp> ( <scp>eDNA</scp> ) focusing on <scp>eDNA</scp> particle size and marker length
复制标题
基于环境 <scp>DNA</scp> (<scp>eDNA</scp>) 微调丰度估计的性能，重点关注 <scp>eDNA</scp> 颗粒大小和标记长度
DOI：
10.1002/ece3.9234
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发表时间：
2022
影响因子：
2.6
通讯作者：
Yamanaka Hiroki
中科院分区：
文献类型：
--
作者：
Jo Toshiaki;Yamanaka Hiroki
可靠的丰度估计是环境DNA（eDNA）分析中的主要挑战，这已经通过考虑eDNA迁移和降解的影响来解决。然而，这些eDNA的空间动态依赖于eDNA的细胞和分子结构，其持久性状态（颗粒大小和DNA片段长度）是必不可少的，以提高丰度估计。为了解决这个问题，我们使用了从两种类型的水族馆实验（针对斑马鱼[Danio rerio]和日本竹荚鱼[Trachurus mackerel]）获得的数据集，并比较了不同eDNA大小分数和目标标记长度之间eDNA浓度和物种丰度之间的关系。我们饲养的鱼在不同的个体数量或生物量密度的实验缸，过滤饲养水使用不同的孔径过滤器，并量化eDNA浓度针对不同的片段长度或遗传区域。因此，两个实验都表明丰度估计的准确性和灵敏度得到了提高（即，当靶向3 - 10 μm粒径级的eDNA时，R2值和线性回归斜率增加）。相反，靶向>10 μm粒径级分的eDNA产生较低的R2值。这一结果表明，当靶向极大的尺寸级分时，eDNA浓度和物种丰度之间的关系可能会恶化。相反，靶标记长度对R2值有负面影响。这项研究提出，eDNA浓度和物种丰度之间的关系依赖于在水中的eDNA的粒径，持久性和空间异质性之间的复杂的相互作用。
Reliable abundance estimation is a primary challenge in environmental DNA (eDNA) analysis, which has been addressed by considering the effects of eDNA transport and degradation. However, these eDNA spatial dynamics depend on the cellular and molecular structure of eDNA, with its persistence state (particle size and DNA fragment length) being essential for improved abundance estimation. To address the issue, we used datasets obtained from two types of aquarium experiments (targeting zebrafish [Danio rerio] and Japanese jack mackerel [Trachurus japonicus]) and compared the relationships between eDNA concentration and species abundance among different eDNA size fractions and target marker lengths. We reared the fish in experimental tanks with different individual numbers or biomass densities, filtered rearing water using different pore size filters, and quantified eDNA concentrations targeting different fragment lengths or genetic regions. Consequently, both experiments showed that the accuracy and sensitivity in abundance estimation were improved (i.e.,R2values and slopes of linear regressions increased) when targeting eDNA at the 3‐ to 10 μm size fraction. On the contrary, targeting eDNA at the >10 μm size fraction yielded a lowerR2value. This result indicates that the relationship between eDNA concentration and species abundance can be worsened when extremely larger size fractions are targeted. Conversely, the target marker length negatively affected theR2value. This study proposes that the relationship between eDNA concentration and species abundance relies on the complex interactions between the particle size, persistence, and spatial heterogeneity of eDNA in water.