eDNA used to detect rare Brazilian frogs

Virginia Gewin

A team of researchers in Brazil has identified traces of DNA from several threatened amphibian species – including one not seen since 1968, putatively assigned to Megaelosia bocainensis – in puddles, ponds, and streams, according to a new study (Mol Ecol 2020; doi.org/10.1111/mec.15594).

The researchers analyzed water samples from six montane sites in the Atlantic Coastal Forest and adjacent cerrado grasslands of Brazil in a search for 30 target amphibian species of concern. In addition to Megaelosia, they successfully detected the DNA of four other at‐risk frog species (Hylodes ornatus,Hylodes regius,Crossodactylus timbuhy, and Vitreorana eurygnatha) as well as two that have disappeared locally (Phasmahyla exilis and Phasmahyla guttata).

The lead author of the study, Carla Lopes, an ecologist at São Paulo State University (São Paulo, Brazil), was pleasantly surprised to find DNA evidence for so many of the target species. Her team's approach consisted of combining environmental DNA (eDNA) metabarcoding with an extensive, painstakingly compiled sequence reference database of the region's amphibians. If anything, our data are conservative, says Lopes, given the numerous steps taken to avoid contamination and false positives or negatives.

“[The authors] seized on an opportunity of having genetic information for species that are presumably very rare in the system”, says Christopher Jerde, who uses eDNA to study fish at University of California–Santa Barbara (Santa Barbara, CA). “So much of our conservation problem is that we don't have adequate funding to look hard enough to understand biodiversity.”

While it's a bit tricky to say how long ago the species may have been present in any waterbody, Lopes says, “laboratory studies that control for light, temperature, and pH suggest DNA traces can be detectable after 25 days”. She further explains that the researchers plan to use the DNA, present in great quantities in three different water samples, to guide the field search for Megaelosia in the coming months. Other next steps, she adds, include using eDNA to detect the presence of the chytrid fungus that has caused widespread amphibian declines and advancing the eDNA technique to determine the abundance of amphibian species.

Jerde, whose recent work demonstrated how eDNA can outperform conventional methods for estimating fish species richness, believes that eDNA will soon offer a more robust means of assessing biodiversity because eDNA technology is advancing so rapidly that it won't be long before “we can take a water sample and look at biodiversity across all of these taxa”.

Thought disappeared from Brazil's Serra dos Órgãos National Park, the spotted leaf frog (Phasmahyla guttata) was detected via eDNA.

L Malagoli

中文翻译：

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派遣

eDNA用于检测稀有的巴西青蛙

弗吉尼亚·盖温

根据一项新的研究（Mol Ecol 2020; doi。），巴西的一组研究人员从水坑，池塘和溪流中发现了几种濒临灭绝的两栖动物物种的DNA痕迹，其中包括自1968年以来从未发现过的，推测是归因于Bocainensis的一种。 org / 10.1111 / mec.15594）。

研究人员分析了来自大西洋沿海森林和巴西邻近的塞拉多草原的六个山地地点的水样，以寻找30种令人关注的目标两栖动物。除巨elo病外，他们还成功检测了其他四种有风险的青蛙物种（Hylodes ornatus，Hylodes regius，Crosdodactylus timbuhy和Vitreorana eurygnatha）的DNA以及在本地消失的两种青蛙（Phasmahyla exilis和Phasmahyla guttata）。

该研究的主要作者，圣保罗州立大学（巴西圣保罗）的生态学家卡拉·洛佩斯（Carla Lopes）惊讶地发现了这么多目标物种的DNA证据。她的团队的方法包括将环境DNA（eDNA）元条形码与该地区两栖动物的广泛，精心编写的序列参考数据库相结合。洛佩斯说，考虑到采取了许多步骤来避免污染和假阳性或假阴性，我们的数据是保守的。

“ [作者]抓住了一个机会，为可能在系统中非常稀有的物种提供了遗传信息，”克里斯托弗·杰德说，他使用eDNA在加利福尼亚大学圣塔芭芭拉分校（加利福尼亚州圣塔芭芭拉分校）研究鱼类。“我们保护的主要问题是我们没有足够的资金来看起来很难理解生物多样性。”

洛佩斯说，要说该物种在任何水体中存在多久还有些棘手，但“控制光，温度和pH值的实验室研究表明，在25天后就可以检测到DNA痕迹”。她进一步解释说，研究人员计划在接下来的几个月中使用大量存在于三种不同水样中的DNA来指导野外寻找Megaelosia。她补充说，其他下一步包括使用eDNA检测引起广泛两栖动物下降的乳糜菌的存在，并推进eDNA技术来确定两栖动物物种的丰度。

杰德（Jerde）的最新工作证明了eDNA如何胜过估计鱼类物种丰富度的传统方法，他相信eDNA很快将提供一种评估生物多样性的更可靠的方法，因为eDNA技术发展如此之快，以至于不久之后“我们可以采取水样本并研究所有这些分类单元中的生物多样性。”

想法从巴西的塞拉·多斯·奥尔加斯国家公园（Serra dosÓrgãosNational Park）消失了，通过eDNA检测到了斑蛙（Phasmahyla guttata）。

马拉戈利