数百万年的DNA重写了猛mm象的进化树

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古代DNA彻底改变了我们对人类进化的理解方式,揭示了人口如何迁移和互动,并向我们介绍了诸如Denisovans之类的亲戚。但是,人类并不是唯一一个将DNA遗留骨头中的人,对人类有用的分析方法也可以对任何其他物种使用。

如今,似乎已测序最古老的DNA的帮助下,猛ma象成为了焦点。来自三个古老磨牙的DNA揭示了猛ma象的幽灵世系与远亲杂交,产生了北美猛population象。

古代DNA彻底改变了我们对人类进化的理解方式,揭示了人口如何迁移和互动,并向我们介绍了诸如Denisovans之类的亲戚。但是,人类并不是唯一一个将DNA遗留骨头中的人,对人类有用的分析方法也可以对任何其他物种使用。

如今,似乎已测序最古老的DNA的帮助下,猛ma象成为了焦点。来自三个古老磨牙的DNA(一个可能已超过一百万年)揭示了猛ma象的幽灵世系与远亲杂交,产生了北美猛population象。

猛mm象与人类共享某些东西:像我们一样,它们起源于非洲人口,但遍布地球的大部分地区。由于分布较早,庞然大物的种群花费了足够的时间彼此分开以形成不同的物种。从大象分支之后,猛ma象首先分裂成所谓的南方和草原物种。后来,由于适应了冰河时期的气候,产生了羊毛猛ma象及其近亲北美猛mm象,称为哥伦比亚猛mm象。但是,所有这些物种都已灭绝,唯一的活着的亲戚是大象。

我们从其中两个物种(羊毛和哥伦比亚猛ma)获得了DNA。这些揭示了对寒冷气候的许多适应以及少量的杂交,因为猛ma象进入了北美,对哥伦比亚种群的基因组贡献了少量(约10%)。

这项新的工作集中西伯利亚发现的猛ma牙上,那里的条件既有利于遗骸的保存,又有利于遗骸中所含DNA的保存。牙齿来自似乎是最近冰川期开始时沉积的物质层,那时正是该地区猛ly象族的祖先。

我们没有任何牙齿的确切日期,因为它们似乎太老了,无法进行碳测年。取而代之的是,通过结合矿床中存的物种和已知的地球磁场方向翻转时间来推断日期。此外,牙齿的形状还提供了一些提示,说明它们与哪些种类组合一起,以及何时显示它们的进一步指示。总的来说,一颗牙齿可能至少有500,000年的历史,另一颗牙齿大约有一百万年的历史,还有三分之一仍旧。

以前,从动物遗体中获得的最古老的DNA大约是这些样品中最年轻的年龄。但是,研究人员能够从每个臼齿中回收一些象大象一样的DNA,尽管它们的碎片很严重,而且许多碱基也遭到了破坏。研究人员能够为三颗牙齿中的每一个分离出完整的线粒体基因组,因为每个细胞的线粒体中都包含该基因组的许多副本。但是,只能获得核基因组的片段,最多只能获得一个基因组的大约10%,最坏的是不到2%。 (不到2%的个人基础仍然是数千万。)

利用猛ma象和大象DNA的差异,并假设突变率保持恒定,研究小组能够得出每个离开牙齿的动物必须生存的独立日期。根据线粒体基因组,日期是160万,130万和90万年前。对于两个拥有足够核基因组进行分析的日期,日期是130万和60万年前。这两个样品的基于DNA的日期彼此吻合,并且它们的发现日期也很吻合。最古老的样品可能早于其所的沉积物,因此可能死亡后被转移了。

尽管这些日期尚不确定,但它们很明显地将其中两个样本放置为有史以来从动物身上获得的最古老的DNA。这将意味着这些猛mm象冰河时期盛行后不久就居住西伯利亚,尽管之前没有明显的羊毛猛ma象世系。他们还早于北美著名的猛mm象。

由于所有这些原因,基因组可能对猛ma象的历史有很多话要说。

他们做到了。尽管这两个年轻样本显然早于产生了更完整基因组的最新样本,但它们显然最终产生羊毛猛mm象的同一血统上。但是,最古老的站点来自一个名为Krestovka的站点,看起来完全来自一个单独的世系。尽管它与猛ma象似的分支有关,但显然与它分开了,分析表明这种分裂至少发生180万年前。

克雷斯托夫卡(Krestovka)也没有任何直接的现代后代,这表明它可能已经作为独特的种群而死亡。但是它的许多DNA仍是哥伦比亚猛ma象基因组的一部分。显然,克雷斯托夫卡(Krestovka)之后的某个时候,它的血统与羊毛猛mm的祖先杂交。结果是两个分支的基因组接近50/50的混合,其后代移居北美并形成了哥伦比亚猛mm象种群。直到很长一段时间,当他们进入北美时,才遇到了后裔,这些后裔现是一个独特的羊毛猛mm象种群。

这些动物与后代羊毛猛ma象的适应能力也差不多。研究人员确定了5,600例猛ma象基因组蛋白质与大象蛋白质不同的情况。古老的猛s象已经吸收了其中超过85%的变化,包括与头发生长,脂肪沉积,温度感应以及昼夜周期处理有关的变化。

换句话说,这些东西看起来很像毛毛猛s象,即使它们来自当时仍居住西伯利亚的更大的猛象祖先群体的一部分。

猛mm象可能是一个相对罕见的案例,因为我们有很多遗骸,而且它们生活世界各地,那里的条件非常适合保存DNA。但是它们也可能有很长的世代,因此它们比许多其他物种经历的种群变化要缓慢得多。

即使使这种年龄的DNA稀少,我们也可能不需要古老的DNA来获取有关我们周围物种如何形成的有价值的信息。基于我们和猛ma,深入研究这些历史可能会带来很多惊喜。

自然,2021.DOI:10.1038 / s41586-021-03224-9(关于DOI)。


英文译文:

Ancient DNA has revolutionized how we understand human evolution, revealing how populations moved and interacted and introducing us to relatives like the Denisovans, a "ghost lineage" that we wouldn't realize existed if it weren't for discovering their DNA. But humans aren't the only ones who have left DNA behind in their bones, and the same analyses that worked for humans can work for any other group of species.

Today, the mammoths take their turn in the spotlight, helped by what appears to be the oldest DNA ever sequenced. DNA from three ancient molars, one likely to be over a million years old, has revealed that there is a ghost lineage of mammoths that interbred with distant relatives to produce the North American mammoth population.

Mammoths share something with humans: Like us, they started as an African population but spread across much of the planet. Having spread out much earlier, mammoth populations spent enough time separated from each other to form different species. After branching off from elephants, the mammoths first split into what are called southern and steppe species. Later still, adaptations to ice age climates produced the woolly mammoth and its close relative, the North American mammoth, called the Columbian mammoth. All of those species, however, are extinct, and the only living relatives are the elephants.

We have obtained DNA from two of these species, the woolly and Columbian mammoths. These revealed both a number of adaptations to cold climates and a small degree of interbreeding, as woolly mammoths made their way into North America and contributed a small amount (about 10 percent) to the genome of the Columbia population.

The new work focused on mammoth teeth found in Siberia, where conditions have favored both the preservation of remains and the preservation of the DNA they contain. The teeth come from layers of material that appear to have been deposited at the start of the most recent glacial period, which is when the ancestors of the woolly mammoth population should have been present in the area.

We don't have precise dates for any of the teeth, as they appear to be too old for carbon dating. Instead, dates have been inferred using a combination of the species present in the deposits and the known timing of flips in the orientation of Earth's magnetic field. In addition, the shape of the teeth provides some hints about what species they group with and some further indication of when they were deposited. In all, one tooth is likely to be at least 500,000 years old, another about a million years old, and a third somewhat older still.

Previously, the oldest DNA obtained from animal remains is roughly the age of the youngest of these samples. But the researchers were able to recover some elephant-like DNA from each of the molars, although it was badly fragmented, and many individual bases were damaged. Researchers were able to isolate the full mitochondrial genome for each of the three teeth, as each cell contains many copies of this genome in each of its mitochondria. Only fragments of the nuclear genome could be obtained, however—at most, about 10 percent of one genome, and at worst under 2 percent. (Less than 2 percent is still tens of millions of individual bases.)

Using the differences between the mammoth and elephant DNA and assuming a constant rate of mutation, the research team was able to derive independent dates for when each of the animals that left a tooth must have lived. Based on the mitochondria genome, the dates were 1.6 million, 1.3 million, and 900,000 years ago. For the two that had enough nuclear genome to analyze, the dates were 1.3 million and 600,000 years ago. The DNA-based dates for these two lined up nicely with each other and the date of the material they were found in. The oldest sample might be older than the deposit it's in, and thus it might have been moved after death.

While these dates are fairly uncertain, they pretty clearly place two of the samples as the oldest DNA ever obtained from animals. And it would mean that these mammoths were living in Siberia shortly after ice-age conditions prevailed, although before there was a clear woolly mammoth lineage. They'd also predate the known appearance of mammoths in North America.

For all these reasons, the genomes potentially have a lot to say about the history of mammoths.

And they do. The two younger samples are clearly on the same lineage that eventually produced the woolly mammoth, although they obviously predate the more recent samples that have yielded more complete genomes. But the oldest, from a site called Krestovka, looks like it's from a separate lineage entirely. While it's related to the woolly mammoth branch, it clearly diverged from it, and the analysis suggests that the split occurred at least 1.8 million years ago.

Krestovka also doesn't have any direct modern descendants, indicating that it may have died off as a distinct population. But a lot of its DNA carried on as part of the Columbia mammoth genome. Apparently, at some point after the Krestovka, the lineage it was on interbred with the ancestors of the woolly mammoths. The result was a nearly 50/50 mix of the genomes of the two branches, the descendants of which migrated into North America and formed the Columbia mammoth population. Only much later did it meet the descendants, now a distinct woolly mammoth population, when they crossed into North America.

These animals were also already nearly as well adapted to the cold as their descendants, the woolly mammoths. The researchers identified 5,600 cases where the proteins of the mammoth genome differed from those in elephants. The ancient mammoths had already picked up over 85 percent of these changes, including ones involved in hair growth, fat deposits, temperature sensing, and handling of day/night cycles.

In other words, these things probably looked a lot like woolly mammoths, even if they were from a population that was still part of a larger cluster of mammoth ancestors living in Siberia at the time.

Mammoths may provide a relatively rare case, as we have a lot of their remains, and they lived in a part of the world where conditions are excellent for preserving DNA. But they also likely had a long generation time, so they underwent population changes at a far more gradual pace than many other species.

Even though getting DNA this old is rare, we might not need ancient DNA to get valuable information on how the species around us came into existence. And based on us and the mammoths, digging into these histories may provide lots of surprises.

Nature, 2021. DOI: 10.1038/s41586-021-03224-9  (About DOIs).


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