MIND-BLOWING: 45,000-Year-Old HUMAN DNA Unlocks Clues to Our Past - Archaeological Science Ep 20

Scientists have extracted DNA out of 45,000 year old human bones excavated from two sites in Europe, and found out things about these ancient humans that we can't learn from studying the objects they've left behind or looking at their bones alone. Now Europe 45,000 years ago was a very different world from today's. This was the time of the Stone Age, or Paleolithic era, where the main technology was the creation and use of stone tools. People had to hunt wild animals and gather plants to survive, and anatomically modern humans coexisted with Neanderthals. But our material from the Paleolithic period is very fragmented, and there is so much we don't know in comparison to what we do know. Ancient DNA is helping fill in some gaps and is absolutely changing our understanding of the Paleolithic period because it preserves information that has otherwise been lost to time. So what exactly did scientists find out by studying 45,000 year old human DNA? I'm Madame Archaeologist, your go-to informant on everything archaeology, and in this episode I'll dive into the groundbreaking study that's allowed us to travel back in time to Paleolithic Europe, and I'll show you just what types of fascinating information can be preserved in 45,000 year old genomes. Let's dive in. The samples come from two sites. One genome is from the Konya Prusi Caves in the Czech Republic. It belongs to an adult female labeled Zlaty Kun, after the hill on top of the cave system. The other six genomes come from a site about 230 kilometers away called Ilzenhule in Rannis in Germany, of which three were male labeled Rannis 10, 13, and 87, and three were female labeled Rannis 4, 6, and 12. Both of these places are cave sites and the individuals, as expected, were hunter-gatherers. The Zlaty Kun genome was high coverage and so was one of the Rannis genomes, while the other five, although low coverage, produced enough data to conduct population level studies. The genomes in question were published in this paper. Earliest modern human genomes constrain timing of Neanderthal admixture, although some information on Zlaty Kun was published earlier in this paper, and information on the mitochondrial DNA of the Rannis individuals, more on this later, comes from a separate paper as well. These individuals lived and died around 45,000 years ago, with radiocarbon dates collectively giving us a range of 42,200 to 49,540 Cal BP. This places them close in time to the Ust-Ishim individual from Siberia, whose genome has also been sequenced. He lived somewhere between 43,210 and 46,880 Cal BP, as well as individuals from Bachokhiro in Bulgaria, who lived sometime between 42,580 and 45,930 years ago, but these are for another time. Today I'm just focusing on Zlaty Kun and the Rannis individuals, who, if we go by the radiocarbon date range, represent the oldest anatomically modern humans to have had their genomes published to date. One of the first things the geneticists found was that Zlaty Kun and the Rannis individuals, although buried about 230 kilometers from each other, were genetically related, meaning they shared recent ancestors in their family histories. Zlaty Kun was found to be a 5th or 6th degree relative of Rannis XII and Rannis IV, and was more distantly related to the other Rannis individuals. Some of the Rannis individuals were also closely related. Two of the females, Rannis IV and Rannis VI, were found to be a mother and daughter. If we go just based on DNA, we can't tell who the mother was and who the daughter was, but given that osteological analysis determined that Rannis VI was just a young child when she died, she was less than 5 years old, we can say without a doubt that Rannis IV was the mother and Rannis VI was the daughter. Rannis IV also shared a 2nd or 3rd degree relationship with Rannis XII, with 2nd degree being more likely. This means that they could have been a grandparent and grandchild, and 10 niece, or half-siblings. It can't get more specific than this, but this is still a major feat because you go from having a pile of 45,000 year old bones, to establishing the minimum number of people represented by these bone fragments and who was related to whom there. You can't do this without ancient DNA. Not unexpectedly, the Zlatikun and Rannis individuals all belonged to the same small-sized population, which the researchers conveniently named the Zlatikun-Rannis population. The lineage to which they belonged split, or diverged, from the Out-of-Africa lineage early on following the Out-of-Africa migration, but not before an important admixture event with Neanderthals took place. Yes, this means that our 45,000 year old hunter-gatherers here had some Neanderthal DNA, but I'll get into more details on this later. Now, the Out-of-Africa migration refers to the last major human migration out of the African continent that likely took place roughly 50,000 to 70,000 years ago, and it is this lineage from which all non-African populations today descend. However, genetically, no non-African population today is exactly the same as this population that left the continent tens of thousands of years ago, just as no population today is going to be genetically the exact same as the original Homo sapiens who first emerged about 200,000-300,000 years ago. This is because all of us have accumulated genetic changes since then. As time went on, following the Out-of-Africa migration, populations diverged, or branched off, from this Out-of-Africa lineage. Divergence is an important concept in population genetics. It refers to the accumulation of genetic changes, or mutations, between populations, usually due to a lack of gene flow. When enough changes have accumulated, populations diverge, or split, becoming distinct. The Zlatikun-Ranis population is the earliest, or deepest split, from the Out-of-Africa lineage that we have seen in ancient genomes so far. It split even earlier than the lineages leading to other hunter-gatherers who lived close to Ranis and Zlatikun in time, and who have had their genomes sequenced, of course, such as Bachokiro, Ustishim, and Tianyuan. However, this does not mean that the Zlatikun-Ranis population was the first to split from the Out-of-Africa lineage, but rather that it is the oldest split that we have managed to sample directly. There is another population whose former existence has been hypothesized through the statistical analysis of DNA, called the Basal Eurasians, and their lineage split even earlier from the Out-of-Africa lineage than the Zlatikun-Ranis population did, even prior to the main Neanderthal admixture event. The Basal Eurasians are supposed to have carried little to absolutely no Neanderthal DNA, and then they admixed with later Western Asian populations, diluting the level of Neanderthal ancestry in their descendants. Note that Western Eurasians today, on average, carry less Neanderthal than East Asians, who lack Basal Eurasian ancestry. The Basal Eurasians are a ghost population because we've inferred their former existence through the statistical analysis of DNA, but we haven't directly associated them with any skeletal remains yet. So, the Zlatikun-Ranis population is the earliest to branch off from the Out-of-Africa lineage from all the populations that we have sampled directly, but it wasn't the very first. It is also interesting that the Zlatikun-Ranis population doesn't seem to have left any detectable genetic impact on later ancient or modern day populations, at least out of those we've sampled to date. Their lineage, it appears, died out. Haplogroups were also predicted for them. There are two types, mitochondrial and Y-chromosomal, and they each trace a specific line in someone's ancestry, mitochondrial the direct maternal line and Y-chromosomal the direct paternal line. Everyone inherits mitochondrial DNA from their mother, and so anyone can find out what their mitochondrial haplogroup is, but the Y-chromosome is only found in males, and so only males can directly find out what their Y-chromosomal haplogroup is. If you're a woman and you want to learn about your paternal line, you need your father or a paternal line male relative to take a DNA test. Now, everyone who shares a mitochondrial haplogroup shares a female ancestor on their direct maternal line, and everyone who shares a Y-chromosomal haplogroup shares a male ancestor on their direct paternal line. And if we go back far enough, all of us living today share mitochondrial Eve as the most recent common matrilineal ancestor, and Y-chromosomal Adam as the most recent common patrilineal ancestor. They were not the first homo sapiens to exist, they were not the only humans around at their time, they were not the only people from the very remote past who have left descendants today, and they likely didn't even live at the exact same time. In other words, they were not a couple. Rather, mitochondrial Eve is the most recent female from whom all of us living today are descended from through an unbroken line of mothers, and Y-chromosomal Adam is the most recent male from whom all of us today are descended from through an unbroken line of fathers. If we look at these trees, we see that we start off with mitochondrial Eve and Y-chromosomal Adam, and then haplogroups branch off. Your haplogroup is assigned based on mutations in either your mitochondrial DNA sequence or, if you're male, also your Y-chromosome. These trees focus on the main lineages, your haplogroup will fall into a more specific sub-lineage. Zlatikun and the Rannus individuals lived, in the grand scheme of things, not too long after the Out-of-Africa migration, and so it's expected that they would belong to more ancient non-African haplogroups. In terms of Y-chromosomal haplogroups, one of the Rannus males was assigned to basal haplogroup F, basal meaning an early branch, close to the root of the tree, and then two others were assigned to N-O, within the K2a branch. F is one of the major lineages that is ancestral to most non-African Y-chromosomal haplogroups, including N-O. Again, such ancient predictions are expected, as we are dealing with samples that are more than 40,000 years old. These individuals lived long before haplogroups we hear a lot about today, like R1b, emerged. As for mitochondrial haplogroups, the Zlatikun individual and five of the Rannus individuals fell within the N-clade, while one Rannus individual belonged to haplogroup R. Alongside M, N is one of the macrohaplogroups from which all non-African mitochondrial haplogroups descend. R branched off from N, N is itself ancestral to clades that are more commonly found in Europe at later times, like U and H. Zlatikun in particular only deferred from the ancestral N-haplotype by carrying three additional substitutions and one insertion. Substitutions and insertions refer to two specific types of mutations. Substitution referring to when one nitrogenous base in a DNA sequence has been swapped for another, and insertion to when an extra base has been added. That is what your haplogroup boils down to. Your haplogroup corresponds to the mutations that you carry. Such ancient mitochondrial haplogroups for Zlatikun and Rannus are, again, expected given their very ancient age. Time for the coolest part, Neanderthal DNA. Shortly after the out of Africa migration, humans interbred with Neanderthals, and this has left down to the present day. All non-Sub-Saharan African populations, and even Sub-Saharan Africans who harbor some Eurasian ancestry, have a little bit of Neanderthal DNA. Now, current research suggests that the Neanderthal DNA harbored by people today comes largely from one major admixture event. And although some ancient individuals show signs that they had additional more recent Neanderthal ancestors in their family histories, for example, the more than 40,000-year-old individuals from Bulgaria had some Neanderthal ancestors only a few generations before they lived, this is not the case for all ancient populations who coexisted with the Neanderthals, and today, it is this one main admixture event that has left a detectable impact. If you'd like to learn more about Neanderthals, I recommend checking out my episode, DNA of the Last Neanderthal, where I discuss a DNA study performed on a Neanderthal nicknamed Thorin, who lived close in time to his species' extinction. What the researchers found in Thorin's DNA was completely unexpected, and has taken the study of prehistory in a whole new direction. Now, the high-coverage Rannis individual and Zlatikun carried about 2.9% Neanderthal DNA, and the lower-coverage genomes that were good enough to call for Neanderthal segments had a similar estimate of 2.7 to 3.3%. This is higher than the average European today. This study from 2017 estimated that present-day Western Eurasians carry between 1.8 to 2.4% Neanderthal DNA. Now, we now know that this likely has something to do with Basal Eurasian ancestry diluting the Neanderthal DNA. What's even more fascinating, though, is that despite the fact that the Rannis and Zlatikun individuals co-inhabited Europe with the Neanderthals, the Neanderthal DNA harbored by them comes from the same admixture event that people today can trace the Neanderthal ancestry back to. And this is where the paper has the most impact. Because we have radiocarbon dates, we can use these to refine our estimate of when this important admixture event took place. The researchers chose to use high-coverage Rannis 13 and his radiocarbon date of 43,400 to 46,580 Cal BP for performing calculations. Assuming a generation time of 29 years and estimating the admixture event to have taken place 56 to 98 generations before Rannis 13 lived, the researchers constrained the timing of This is a bit later than previous estimates of 52 to 57,000, 47 to 65,000, and 41 to 54,000 years ago. It is, however, the most up-to-date estimate, and much more precise than these broader figures, because 1. it relies on an ancient sample who lived relatively close in time to the admixture event, and 2. it uses a radiocarbon date as its basis. That said, it would be even better to test this updated estimate against another dataset. If we can sequence another high-coverage genome from the Paleolithic that carried Neandertal DNA from the same admixture event shared with people today and radiocarbon date that remains, we can see if the calculations return similar estimates or not. I'll keep you posted. Finally, geneticists were able to get information on some interesting genes, such as those involved in determining things like whether you're going to be able to digest milk as an adult or what color of your eyes, skin, and hair is going to be. When it comes to digesting milk, an enzyme called lactase helps break down lactose, a sugar that occurs naturally in milk and dairy products, into galactose and glucose, simple sugars that are easier for our bodies to absorb. Lactase is encoded by the lactase gene. This means that the lactase gene provides the instructions for making the lactase enzyme. The expression of the lactase gene, in turn, is primarily controlled by a regulatory region within a nearby gene called MCM6. I'm not going to go into technical details here, but the important thing to know is that a mutation in this regulatory region of MCM6 allows for lactase persistence, that is, the continued production of the lactase enzyme. As babies, we produce lactase naturally in order to digest breast milk, but after weaning, lactase production declines. However, a change in the regulatory region of the MCM6 gene allows for the continued expression of lactase into adulthood. At least five or more SNPs, which is a type of mutation where one nitrogenous base in the DNA sequence has been swapped for another, are associated with lactase persistence, but one of these, RS4988235, is the major variant that allows for lactase persistence in Europeans. The Renaissance Laticune individuals lacked this mutation and so they were likely lactose intolerant, and this is a completely expected finding as our farm animals hadn't been domesticated yet 45,000 years ago. People were not drinking non-human milk during the Middle and Upper Paleolithic, and so there was no need for the continued expression of lactase. Some genes also play a large role in determining what someone's skin, eye, or hair color will be. Overall, darker skin, eyes, and hair were predicted for Zlatikun and the Renaissance individuals. However, some information was missing. For example, genes SLC24A5 and SLC45A2 are the two most important genes associated with lighter skin pigmentation in Western Eurasians today, and while there was information published here on gene SLC45A2, information on gene SLC24A5 was missing. It doesn't look like it was tested at all. It is likely that Zlatikun and the Renaissance individuals, given their age, would not have carried the light skin version of this gene, as it is estimated to have arisen about 22,000 to 28,000 years ago. That's long after Zlatikun and the Renaissance individuals lived. However, this estimate is based on current research and we are constantly refining our picture as more ancient genomes get tested, and so it would have been better if the researchers had gotten information on this gene as well. Even if the Zlatikun-Renaiss population came back and carried the ancestral version of the gene, I would have liked to have had that direct information reported because then we can say, without an ounce of doubt, that 45,000 years ago, hunter-gatherers in Europe were carrying the ancestral form of the gene. So, what did researchers find out by studying DNA from 45,000-year-old modern humans, buried in two places 230 kilometers apart? They found that all the individuals belong to the same genetic population, that this population is the earliest split from the Out-of-Africa lineage directly sampled so far, that Zlatikun was distantly related to the Renaissance individuals, that they carried roughly 3% Neanderthal DNA, that this Neanderthal DNA comes from the same main admixture event that left an impact on the DNA of many present-day populations and that this admixture took place roughly 45,000 to 49,000 years ago, that they belonged to mitochondrial haplogroups N and R and the males to Y-chromosomal haplogroups F and N-O, that they probably had darker skin, eyes, and hair color, and that they were lactose intolerant, which is expected given that animals haven't been domesticated yet. This may not be everything we can learn about individuals, but it's certainly a lot of information that we can't glean from just looking at their bones. As usual, if you have any thoughts, feel free to leave a comment, subscribe for more cool content via your go-to informant on everything archaeology, Madam Archaeologist.