Individual haplotyping of whale sharks from seawater environmental DNA
Individual haplotyping of whale sharks from seawater environmental DNA
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DOI：
10.1111/1755-0998.13451
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发表时间：
2021-07-16
影响因子：
7.7
通讯作者：
Meekan, Mark
中科院分区：
文献类型：
--
作者：
Dugal, Laurence;Thomas, Luke;Meekan, Mark
种群遗传数据可以为物种的人口统计学提供有价值的信息。对于稀有和难以捉摸的海洋巨型动物，用于生成数据的样本传统上是从组织活检中获得的，这可能在后勤上困难且昂贵，并且需要侵入性采样技术。环境DNA （eDNA）分析提供了一种替代的、微创的方法来提供重要的遗传信息。尽管在元条形码研究中，eDNA方法已被广泛用于物种检测和生物多样性监测，但该技术在解决种群水平问题方面的潜力仍未得到充分探索。在这里，我们应用“eDNA单倍型”来估计澳大利亚宁格罗礁（Ningaloo reef）鲸鲨（Rhincodon typus）聚集的种内遗传多样性。在两周的时间里，我们收集了鲨鱼背后的海水样本，然后从同一只动物身上采集了组织活检样本。我们的数据显示，在所有28个样本中，eDNA和组织样本中恢复的mtDNA序列100%匹配。在海水样本中，>97%的所有reads被分配到6个显性单倍型，并且在每个样本中都恢复了一个明确的显性信号（类似于99%的样本reads）。我们的研究证实了海水eDNA在个体水平上的准确单倍型。当来自一个个体的DNA明显支配每个eDNA样本时，它为群体遗传分析提供了许多与组织样本相同的机会，潜在地消除了对组织样本的需要。我们的研究结果表明，用于种群水平分析的eDNA方法有可能为海洋巨型动物的保护和管理提供关键的人口统计数据。
Population genetic data can provide valuable information on the demography of a species. For rare and elusive marine megafauna, samples for generating the data are traditionally obtained from tissue biopsies, which can be logistically difficult and expensive to collect and require invasive sampling techniques. Analysis of environmental DNA (eDNA) offers an alternative, minimally invasive approach to provide important genetic information. Although eDNA approaches have been studied extensively for species detection and biodiversity monitoring in metabarcoding studies, the potential for the technique to address population-level questions remains largely unexplored. Here, we applied "eDNA haplotyping" to obtain estimates of the intraspecific genetic diversity of a whale shark (Rhincodon typus) aggregation at Ningaloo reef, Australia. Over 2 weeks, we collected seawater samples directly behind individual sharks prior to taking a tissue biopsy sample from the same animal. Our data showed a 100% match between mtDNA sequences recovered in the eDNA and tissue sample for all 28 individuals sampled. In the seawater samples, >97% of all reads were assigned to six dominant haplotypes, and a clear dominant signal (similar to 99% of sample reads) was recovered in each sample. Our study demonstrates accurate individual-level haplotyping from seawater eDNA. When DNA from one individual clearly dominates each eDNA sample, it provides many of the same opportunities for population genetic analyses as a tissue sample, potentially removing the need for tissue sampling. Our results show that eDNA approaches for population-level analyses have the potential to supply critical demographic data for the conservation and management of marine megafauna.