The Two Stories of Neanderthals

  Neanderthals are relatives of our ancestor Homo sapiens. Scientists have long believed that Neanderthals were replaced by Homo sapiens tens of thousands of years ago and left no descendants. However, in recent years, scientists have discovered through the study of “ancient DNA” that genes from Neanderthals are mixed in the genome of modern humans. This shows that in ancient times, there was some degree of interbreeding between Homo sapiens and Neanderthals. Studying the relationship between Homo sapiens and Neanderthals is of great significance for understanding the evolutionary history of human beings.
  This year’s Nobel Prize winner in Physiology or Medicine Swante Pabo is one of the founders of the field of “ancient DNA” research. “Ancient DNA” refers to the DNA contained in the remains of ancient organisms thousands or even tens of thousands of years ago. By studying these “ancient DNA”, many questions about the evolution of species can be answered. In Pabo’s book “Neanderthals” (Chinese version published in 2018), the author introduced how he started a road of “ancient DNA” research through a whimsical idea 40 years ago.
Crazy Ideas and Failed Research

  Pabo’s “Neanderthal” not only gives the conclusions of a series of scientific researches, but also shows readers the course of scientific discoveries. In describing scientific discoveries, the author does not hide the difficulties he encountered or the mistakes he made. For example, Pabo was initially fascinated by studying the DNA of ancient Egyptian mummies. At that time, he was studying for a doctorate, studying proteins related to human immunity, and it was undoubtedly a crazy idea to suddenly turn to the study of ancient human DNA. In order to achieve his research goals, Paabo risked offending his supervisor and took a lot of time from his doctoral research to collect mummy samples at a museum in what was then East Germany. Through a series of experiments, he thinks he has extracted the DNA of an ancient mummy. Pabo’s research results have also been published in some academic journals, including the famous academic journal “Nature” that many researchers envy. However, later research found that “ancient DNA” was actually easily contaminated by DNA from modern humans. Since Pabo did not consider this issue at that time, and did not design a plan to control pollution, the “mummy DNA” he extracted in the first few times is likely to be the result of contamination by modern human DNA.
  What enlightenment will Pabo’s experience in studying “ancient DNA” bring us? First, crazy ideas are often the beginning of great undertakings; second, the difficulties to be overcome to truly advance in science are unimaginable. Sometimes you feel that your research has made a breakthrough, but because some key factors are not considered, the experimental results will be wrong. As far as the field of “ancient DNA” is concerned, in the early 1990s, with the development of gene cloning technology, a large number of scientists entered this field in an attempt to clone ancient DNA. During that time, the news coverage was increasingly gruesome. It has been reported that scientists have cloned the DNA of all kinds of ancient creatures by using various fossils tens of millions of years ago, including plants, yeast, termites, dinosaurs, and so on. However, over time, the results of these experimental cloning studies were proven wrong. DNA cannot survive for tens of millions of years, and these so-called ancient DNAs are actually pollution from bacteria.
Mitochondrial DNA from extinct animals

  During the high-profile period of cloning technology, Pabo adjusted his research direction and gradually focused his work on some problems that could be solved. Since it is difficult to distinguish the DNA of modern humans from the DNA of ancient humans, we will not study human DNA for the time being, but turn to the study of some recently extinct animals. Another advantage of studying these animals is that they became extinct relatively recently (thousands to tens of thousands of years ago), and researchers do not need to purify DNA from hundreds of thousands or millions of years ago. This “do what you can” attitude quickly paid off.
  Pabo first studied mitochondrial DNA. Mitochondria are organelles in the cell that serve as the cell’s energy supply station. Organisms such as animals, plants, and fungi are called eukaryotes because they are all composed of eukaryotic cells, and eukaryotic cells have mitochondria in them. During the evolution of eukaryotic cells, due to the acceptance of ancient bacteria, mitochondria gradually evolved. Although most of the mitochondrial DNA has now been transferred to the nucleus, some DNA remains in the mitochondria. Because of the large number of mitochondria in a cell, which are also protected by a double membrane, it is much easier to extract mitochondrial DNA than to extract the DNA in the nucleus from ancient samples.
  Pabbo’s first study subject was the molar, a sloth-like animal that became extinct 10,000 years ago. Unlike sloths, gyrodons live on the ground. Through the analysis of ancient mitochondrial DNA, Pabo led the research team to establish the genetic relationship between the molar and the living two-toed sloth. Extant three-toed sloths are more distantly related. Thus, this study suggests that the two extant species of sloth may have independently evolved an arboreal lifestyle.
From Rodons to Humans

  After a successful start, Paabo began to consider studying Neanderthal DNA. Because although Neanderthals belong to human beings, they are different from modern humans (descendants of Homo sapiens) after all. Therefore, the pollution problem of modern human DNA is also easier to deal with on Neanderthal DNA samples; at the same time, by comparing the differences between Neanderthal DNA and modern human DNA, many questions about human evolution can be answered.
  Like the rodent study, Pabo extracted and analyzed Neanderthal mitochondrial DNA. After comparing with the mitochondrial DNA of modern humans, Pabo obtained the preliminary research results that “Neanderthals did not contribute to the mitochondrial DNA of modern humans.”

  What does this mean? Pabo’s research results mainly cover two possibilities. One is that Neanderthals did not have a history of interbreeding with Homo sapiens, and the other is that their offspring were sterile or had some kind of defect, so they were eventually eliminated. But because mitochondrial DNA doesn’t necessarily tell the whole story, there are other possibilities lurking in the findings.
  Mitochondria are only found in the cytoplasm, so it can only be inherited through the maternal line. In other words, if male Neanderthals and female Homo sapiens reproduce, the mitochondrial DNA of Neanderthals will not enter the gene pool of modern humans. Therefore, a comprehensive study of this question will require the purification and analysis of Neanderthal nuclear DNA.
  Purifying nuclear DNA was very difficult, and Pabo tried many methods. First, through various efforts, Pabo and his research team obtained the help of a museum in Croatia to obtain ancient bone samples with particularly high DNA content of Neanderthals. Second, they took advantage of the sequence differences between bacterial and human DNA and treated the samples with enzymes that specifically cut bacterial sequences, thereby greatly enriching the samples for Neanderthal DNA. Finally, Pabo’s team sequenced the samples using the most advanced sequencing technology at the time, known as next-generation sequencing. After overcoming many challenges and trying a variety of cutting-edge technologies, Pabo’s team finally completed the DNA sequencing of Neanderthals.
  After the sequencing is complete, the short DNA sequences measured need to be assembled into the Neanderthal genome, which is also full of challenges. For example, after a long period of time, the bases of Neanderthal DNA may undergo chemical damage, resulting in sequence changes (such as C through deamination to U, which will be read as T when sequencing), So when genetic sequences from Neanderthals differ from modern humans, scientists must determine whether this is a true sequence difference or an alteration due to base damage. At the same time, because the danger of contamination always exists, during the period of analyzing the data, Pabo was frightened many times by the possible serious contamination of the samples, and almost lost control of his emotions. However, rigorous analysis proved that the samples purified by Pabo’s team were of high purity, with less than 1% of DNA from contamination.
  Finally, the results of Pabo’s team proved that among modern humans outside of Africa, Neanderthals contributed to their DNA, and their contribution accounted for about 2% of the modern human genome.
  What is more interesting is that in the DNA of Chinese and Europeans, the contribution of Neanderthals is basically the same. Since no traces of Neanderthal activities were found in China at that time, the explanation given in the book is that when Homo sapiens came out of Africa, they first coexisted with the local Neanderthals in the Middle East for a period of time, During that time, there was some genetic exchange between the two species of humans.
  It is particularly worth mentioning that in the genome of modern humans outside Africa, there is a specific mutation of the MHC gene, which is also common in Neanderthals. Since this MHC gene mutant does not exist in African Homo sapiens, it is likely that the MHC gene mutant of modern humans came from Neanderthals. The researchers found that MHC genes are closely related to the human immune system and are involved in the recognition of antigens, which can recognize certain pathogens outside of Africa. Thus, MHC gene mutants have expanded in modern humans outside of Africa. Although Neanderthals did not travel with Homo sapiens and have reproduced to this day, they have left special gifts in the DNA of modern humans that help them survive.
  In “Neanderthals,” Paabo tells readers two stories. One is a story about science, that is, how to build “ancient DNA” research into a discipline from scratch. The other is a story about our human ancestors, that is, the Neanderthals have not completely “extinct”, and their genes are still continuing through the reproduction of modern humans, silently affecting our lives. These two stories are wonderfully combined into a whole in one book, creating a rich and wonderful space for thinking, which makes readers immerse themselves in it and never forget to return.