2017.04.27提取古人类的DNA

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科学家们现在可以从洞穴的泥土中提取古人类的DNA了
这项技术将使研究人员能够在不依赖化石的情况下研究尼安德特人和其他史前人类。

作者：Ed Yong

贝基-米勒在Trou al'Wesse收集沉积物（Monika V. Knul）。
2017年4月27日

大约4.5万年前，在比利时的一个山洞里，一个尼安德特人死亡。随着它身体的腐烂，它的细胞分裂开来，将其内容物洒落在洞穴地板上。这些残余物包括尼安德特人的DNA，其中一些粘附在沉积物的矿物上。在那里，DNA被拴在岩石上，在它的主人的身体消失和骨头被拾荒者运走后的很长一段时间里，它仍然存在。而在2015年，一群科学家把它挖了出来。

来自马克斯-普朗克进化人类学研究所的Viviane Slon和她的同事们现在已经成功地从长达24万年的沉积物中提取并测序了古代动物的DNA。通过这样做，他们可以推断出尼安德特人、丹尼索瓦人和其他已灭绝的人类的存在，而不需要找到他们的骨头。"我们对它的效果感到惊讶，"斯隆说。"成功率是惊人的。"

"我绝对喜欢这个，"在堪萨斯大学研究古代DNA的Jennifer Raff说，他没有参与这项研究。"虽然人们从沉积物中恢复古代DNA的工作已经有几年了，但这在范围和成功方面都是前所未有的。我在论文上的笔记充满了感叹号。毛犀牛! 长毛象！长毛象！长毛象 洞熊! 尼安德特人和丹尼索瓦人！"

动物有一个巨大的遗传光环，超越它们的肉体，延伸到它们周围的世界。它们的DNA以粪球的形式落在地上，以吸血昆虫的形式在空中飞舞，并在分解过程中渗入土壤。研究活体动物的科学家们已经利用这种环境DNA（eDNA）来识别从大象到蚯蚓的一切。他们可以对自然界进行普查，而不需要发现任何实际的动物--当在难以到达的栖息地处理稀有或难以发现的物种时，这是一个福音。

大约15年来，古生物学家一直试图用同样的技术来研究史前的生物。例如，就在去年，来自加州大学圣克鲁兹分校的贝丝-夏皮罗和她的同事利用沉积DNA来弄清生活在阿拉斯加圣保罗岛的倒数第二组猛犸象何时以及为何灭绝。像这样的研究打破了对化石的传统依赖，因为化石可能很难找到，或者可能根本就没有形成。"夏皮罗解释说："如果一个人必须依靠寻找骨头，那么他将总是有不完整的数据。"但是通过直接从沉积物中分离出DNA，我们可以极大地扩展我们对人类（或其他物种）在哪里，他们何时到达那里，以及他们停留了多久的了解。"

"这是对我们领域中一些伦理难题的解决方案。"
Slon的团队现在是第一个直接从沉积物中成功恢复古人类DNA的团队。他们从欧洲和亚洲已知有尼安德特人或丹尼索瓦人居住的七个地点收集样本，并对样本进行化学处理，以释放被困的DNA。在沉积物中，绝大部分的DNA将来自土壤中的细菌和其他微生物。只有一小部分来自动物。为了得到这一部分，研究小组创造了专门识别哺乳动物DNA的分子，他们可以用这些分子从人群中捞出这些序列。

他们专注于线粒体DNA--位于主要基因组之外的一小簇基因，由于它的数量非常多，所以更容易找到。为了检查这些DNA链是否真正古老，而不是古生物学家自己丢弃的遗传物质的碎片，研究小组寻找了在DNA放置数千年后积累的独特的损伤类型。

除了来自猛犸象、毛犀牛和洞熊的DNA之外，Slon还从四个洞穴中找到了尼安德特人的线粒体DNA--西班牙的El Sidrón、俄罗斯的Chagyrskaya和Denisova洞穴以及比利时的Trou Al'Wesse。第三个地点特别有趣。我们知道尼安德特人使用过Trou Al'Wesse，因为他们留下了工具和被屠宰的动物骨头，但他们的可见遗体从未被发现过。然而，他们的分子遗迹仍在那里。

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在丹尼索瓦洞，研究小组还发现了该地名的DNA--丹尼索瓦人。这些人类的唯一已知化石是来自同一洞穴的一根指骨和两颗牙齿。2010年，斯隆的同事在斯万特-帕博（Svante Paabo）的带领下，对这些标本的线粒体DNA进行了测序，并意识到它们属于一种以前未知的人种。就这样，世界发现了丹尼索瓦人的存在，我们通过他们的DNA比通过他们的骨头了解了更多关于他们的信息。Slon的工作延续了这一传统--她在沉积物中发现了丹尼索瓦人的DNA，这些沉积物比任何出土的化石都要古老。"她说："这证明丹尼索瓦人占领洞穴的时间比我们想象的要早几万年。

现在他们知道他们的技术是有效的，该团队可以在世界没有发现化石的地方，或者人类的历史存在不明确的地方检查人类的DNA。例如，夏皮罗想看看阿拉斯加路线上的沉积物，人类很可能在殖民美洲的路上走过。"她说："这是一个非常有用的工具，它将增强未来的考古研究。

即使有化石存在，也很难在不粉碎化石的情况下从中提取DNA。Slon的工作解决了这个问题。"拉夫说："一些后裔社区可以接受我们对他们的祖先进行遗传学研究，但不能接受为了获得DNA而破坏他们遗体的任何部分。"但是这种方法使我们能够恢复古代的DNA，而不需要破坏遗体。这是一个解决我们领域中一些伦理难题的办法。"

埃德-永是《大西洋》杂志的一名职员作家。他因对COVID-19大流行病的报道而获得普利策解释性报道奖。



Scientists Can Now Pull the DNA of Ancient Humans Out of Cave Dirt
The technique will allow researchers to study Neanderthals and other prehistoric people without relying on fossils.

By Ed Yong

Becky Miller collects sediment from Trou al'Wesse (Monika V. Knul)
APRIL 27, 2017
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Around 45,000 years ago, in a Belgian cave, a Neanderthal died. As its body decayed, its cells split apart, spilling their contents onto the cave floor. Those remnants included the Neanderthal’s DNA, some of which stuck to minerals in the sediment. There, leashed to the very rock, the DNA persisted, long after its owner’s body had disappeared and its bones had been carted off by scavengers. And in 2015, a group of scientists scooped it up.

Viviane Slon from the Max Planck Institute for Evolutionary Anthropology and her colleagues have now managed to extract and sequence the DNA of ancient animals from sediment that’s up to 240,000 years old. By doing so, they can infer the presence of Neanderthals, Denisovans, and other extinct hominids without ever having to find their bones. “We were surprised by how well it works,” says Slon. “The success rates were amazing.”

“I absolutely loved this,” says Jennifer Raff, who studies ancient DNA at the University of Kansas, and who was not involved in the study. “Although people have been working on recovering ancient DNA from sediments for a few years now, this is unprecedented in scope and success. My notes on the paper are full of exclamation marks. Woolly rhinoceros! Woolly mammoth! Cave bear! Neanderthal and Denisovans!”

Animals have a vast genetic aura that extends beyond their physical bodies into the world around them. Their DNA falls to the ground in balls of dung, zips through the air in blood-sucking insects, and leaches into the soil during decomposition. Scientists who study living animals have used this environmental DNA (eDNA) to identify everything from elephants and earthworms. They can conduct a census of the natural world without needing to spot any actual animals—a boon when working with rare or hard-to-spot species in inaccessible habitats.

For about 15 years, paleontologists have tried to use the same technique to study the creatures of prehistory. Just last year, for example, Beth Shapiro from the University of California, Santa Cruz and her colleagues used sedimentary DNA to figure out when and why the second-to-last group of mammoths, which lived on St. Paul Island in Alaska, went extinct. Studies like these break the traditional reliance on fossils, which can be hard to find, or may have never formed at all. “If one must rely on finding bones, one will always have incomplete data,” explains Shapiro. “But by isolating DNA directly from sediments, we can dramatically expand what we know about where people (or other species) were, when they got there, and how long they stayed.”

“It’s a solution to a number of ethical conundrums in our field.”
Slon’s team is now the first to successfully recover the DNA of ancient humans directly from sediments. They collected samples from seven sites in Europe and Asia, where Neanderthals or Denisovans are known to have lived, and chemically treated their samples to liberate the trapped DNA. In sediment, the vast majority of DNA will come from bacteria and other microbes in the soil. Only a small fraction comes from animals. To get at that bit, the team created molecules that specifically recognize mammalian DNA, that they could use to fish those sequences out of the crowd.

They focused on mitochondrial DNA—a small cluster of genes that sits outside the main set, and is easier to find because it’s so abundant. And to check that these DNA strands were genuinely ancient, and not bits of genetic material dropped by the paleontologists themselves, the team looked for the distinctive types of damage that accumulate as DNA sits around for thousands of years.

In addition to DNA from mammoths, woolly rhinos, and cave bears, Slon recovered the mitochondrial DNA of Neanderthals from four caves— El Sidrón in Spain, the Chagyrskaya and Denisova Caves in Russia, and Trou Al’Wesse in Belgium. That third site is especially interesting. We know Neanderthals used Trou Al’Wesse because of the tools and butchered animal bones that they left behind, but none of their visible remains have ever been found. Their molecular remains, however, are still there.

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At Denisova Cave, the team also found the DNA of the site’s namesake—the Denisovans. The only known fossils of these hominids are a finger bone and two teeth from the same cave. In 2010, Slon’s colleagues, led by Svante Paabo, sequenced the mitochondrial DNA from these specimens and realized that they belonged to a previously unknown hominid. That was how the world discovered the existence of Denisovans, and we have learned more about them through their DNA than through their bones. Slon’s work continues that tradition—she found Denisovan DNA in sediment that’s far older than any of the unearthed fossils. “It’s evidence that Denisovans occupied the cave for tens of thousands of years earlier than we thought,” she says.

Now that they know their techniques work, the team can check for hominid DNA in parts of the world where no fossils have been found, or where the historical presence of humans is unclear. For example, Shapiro wants to look at sediments across the Alaska routes that humans likely took on their way to colonizing the Americas. “This is a fantastically useful tool that will empower future archaeological research,” she says.

Even when fossils are present, it’s hard to extract DNA from them without pulverizing them in the process. Slon’s work gets around that problem. “Some descendant communities are okay with us doing genetics research on their ancestors, but not okay with destroying any part of their remains in order to obtain DNA,” says Raff. “But this approach allows us to recover ancient DNA without having to destroy remains. It’s a solution to a number of ethical conundrums in our field.”

Ed Yong is a staff writer at The Atlantic. He won the Pulitzer Prize for Explanatory Reporting for his coverage of the COVID-19 pandemic.