The first complex cells had genes from a complex mix of species

首批复杂细胞拥有来自多种物种的复杂基因混合体

We tend to view ourselves and the complex cells that build us as a distinct branch of the tree of life from the compact, seemingly featureless cells of bacteria and archaea. But we’ve found that our genome is actually a hybrid, a mish-mash of genes from bacteria and archaea, along with some that have evolved in our own lineage. 我们倾向于将自己以及构成我们的复杂细胞视为生命之树上一个独特的分支，与细菌和古菌那种紧凑、看似缺乏特征的细胞截然不同。但我们发现，我们的基因组实际上是一个混合体，是来自细菌和古菌的基因大杂烩，其中还包含了一些在我们自身谱系中进化出来的基因。

Scientists gradually settled on a simple explanation for this: the first complex cells were the product of a fusion between archaeal cells and bacteria, with the bacteria ultimately evolving into the mitochondria, a chemical-power-generating structure that still retains a bit of its own genome. Over time, many of the other bacterial genes were transferred to the nucleus of what was becoming what we now call a eukaryote, intermingling with the archaeal genes there. 科学家们逐渐达成了一个简单的解释：首批复杂细胞是古菌细胞与细菌融合的产物，细菌最终进化成了线粒体——一种至今仍保留着少量自身基因组的化学能量生成结构。随着时间的推移，许多其他细菌基因被转移到了后来被称为“真核生物”的细胞核中，并与那里的古菌基因相互融合。

But a new study has taken a careful look at some of the genes shared by all eukaryotes and comes to the conclusion that the reality is a little more complicated and that there were several waves of gene transfers from bacteria. The big picture of a merger between bacteria and archaea is still right, but it was only part of a picture where gene transfers among species were commonplace. 然而，一项新的研究仔细审视了所有真核生物共有的部分基因，得出的结论是：事实要复杂得多，且存在多轮来自细菌的基因转移。细菌与古菌合并的大框架依然正确，但这只是基因在物种间频繁转移这一宏大图景的一部分。

Clouding the big picture

模糊的宏观图景

The road to the current picture was complicated. For starters, it took ages for anyone to even recognize that archaea were a distinct lineage. And the big advocate for mitochondria being the product of bacteria taking up residence in a different cell was laughed at for a number of years before her ideas became widely accepted, after which she started arguing that every complex structure inside eukaryotic cells had come about through similar processes. (There’s no evidence this is the case.) 通往当前认知的道路十分曲折。首先，人们花了很长时间才意识到古菌是一个独特的谱系。而那位主张线粒体是细菌在另一个细胞中定居产物的倡导者，在她的观点被广泛接受之前，曾被嘲笑了多年；此后，她又开始主张真核细胞内的每一个复杂结构都是通过类似过程产生的。（目前没有证据支持这一点。）

Over time, especially as genome sequences became widely available, it became clear that the mitochondria’s genes, both the ones in their tiny remaining genome and the ones that are now found in our cells’ nucleus, originated in a bacterial lineage called alphaproteobacteria. But figuring out what had swallowed the alphaproteobacteria in the first place took a while longer. 随着时间的推移，特别是基因组序列变得广泛可用后，人们清楚地认识到，线粒体的基因——无论是其残留的微小基因组中的基因，还是现在存在于我们细胞核中的基因——都起源于一种名为“α-变形菌”的细菌谱系。但要弄清楚最初究竟是什么吞噬了α-变形菌，则花费了更长的时间。

Suspicion fell on the archaea, but there are some key biochemical differences between them and us, and known archaea lacked even rudimentary versions of many of the systems that are key features of eukaryotes. Plus, there were no archaeal genomes that were especially close to those of eukaryotes. That only changed about a decade ago. 怀疑对象指向了古菌，但它们与我们之间存在一些关键的生化差异，且已知的古菌甚至缺乏许多作为真核生物关键特征的系统的原始版本。此外，当时也没有发现与真核生物基因组特别接近的古菌基因组。这种情况直到大约十年前才有所改变。

After researchers developed the ability to assemble entire genomes from environmental samples without first separating out different cell types, they discovered the Asgard archaea, a group so closely related to eukaryotes that it led people to ask whether we shouldn’t just consider eukaryotes an elaborate branch of the archaea. 在研究人员开发出无需预先分离不同细胞类型、即可从环境样本中组装完整基因组的技术后，他们发现了“阿斯加德古菌”（Asgard archaea）。这一类群与真核生物的亲缘关系如此之近，以至于人们开始质疑：我们是否应该直接将真核生物视为古菌的一个复杂分支？

The first eukaryotes

首批真核生物

That’s the situation that a group of Barcelona-based researchers decided to wade into. Their first step was to limit the number of species included in the eukaryotic family tree. The species we’ve sequenced tend to be heavily weighted toward animals and species found in familiar environments, resulting in an overrepresentation of some branches of the family tree. The team selected species that resulted in a more even distribution of samples across the tree. 这就是巴塞罗那的一组研究人员决定深入研究的课题。他们的第一步是限制真核生物家谱中包含的物种数量。我们测序的物种往往严重偏向于动物和常见环境中的物种，导致家谱中某些分支的代表性过高。该团队选择了能使样本在生命之树上分布更均匀的物种。

Within the genomes they kept, they got rid of any genes that would produce what they termed “low complexity” proteins—think of something that repeated short stretches of the same amino acids many times. A lot of eukaryotic genes are also close relatives of one another, brought about by multiple duplications of an ancestral gene. The researchers only kept one gene from these collections of related proteins. This resulted in a much smaller group of genes than are present in a typical eukaryotic genome. 在保留的基因组中，他们剔除了任何会产生所谓“低复杂度”蛋白质的基因——即那些多次重复相同氨基酸短序列的蛋白质。许多真核基因也是彼此的近亲，这是由祖先基因多次复制产生的。研究人员从这些相关的蛋白质集合中只保留了一个基因。这使得最终的基因组规模远小于典型的真核生物基因组。

Once all of that was done, they repeated the process two more times, making different choices each time such that over half of the genes in each of the groups differed from the ones in any of the other groups. (Amusingly, the groups of genes in each were termed “orthologous groups,” leading to a lot of the paper talking about “OGs.”) 完成这些工作后，他们又重复了两次该过程，每次都做出不同的选择，使得每组中超过一半的基因与其他组的基因不同。（有趣的是，这些基因组被称为“直系同源组”，导致论文中大量使用了“OGs”这一缩写。）

Looking through the functions of the genes that were present in these simplified genomes, the researchers could make some estimates of what sorts of genetic functions were present in the last common ancestor of all eukaryotes. Their conclusion is that the organism lived in an oxygen-containing environment and harvested energy either by eating other living things or feeding on their remains. 通过审视这些简化基因组中存在的基因功能，研究人员能够推测出所有真核生物的最后共同祖先具备哪些遗传功能。他们的结论是，该生物生活在含氧环境中，通过捕食其他生物或以其残骸为食来获取能量。

These cells already had complex interiors, with internal protein trackways traversed by motor proteins that move cargo within the cell. There were structures (lysosomes and peroxisomes) meant to digest proteins within the cells, and all the basics of eukaryotic metabolism, DNA replication, and RNA production. One of the big features that was absent was sets of genes used to determine when a cell should divide and manage the events that need… 这些细胞已经拥有复杂的内部结构，包括由马达蛋白穿梭其间、用于在细胞内运输货物的内部蛋白质轨道。细胞内存在用于消化蛋白质的结构（溶酶体和过氧化物酶体），并具备了真核生物代谢、DNA复制和RNA生产的所有基础。但缺失的一个重要特征是用于决定细胞何时分裂以及管理相关事件的基因集……