A new paper reveals that a 2012 analysis of Ötzi the Iceman's genome was contaminated and that rather than having steppe ancestry, that he was an almost pure European Neolithic farmer with quite dark skin (as was typical at the time).
In 2012, scientists compiled a complete picture of Ötzi’s genome; it suggested that the frozen mummy found melting out of a glacier in the Tyrolean Alps had ancestors from the Caspian steppe . . . The Iceman is about 5,300 years old. Other people with steppe ancestry didn’t appear in the genetic record of central Europe until about 4,900 years ago. Ötzi “is too old to have that type of ancestry,” says archaeogeneticist Johannes Krause of the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany. The mummy “was always an outlier.”
Krause and colleagues put together a new genetic instruction book for the Iceman. The old genome was heavily contaminated with modern people’s DNA, the researchers report August 16 in Cell Genomics. The new analysis reveals that “the steppe ancestry is completely gone.”About 90 percent of Ötzi’s genetic heritage comes from Neolithic farmers, an unusually high amount compared with other Copper Age remains. . . The Iceman’s new genome also reveals he had male-pattern baldness and much darker skin than artistic representations suggest. Genes conferring light skin tones didn’t become prevalent until 4,000 to 3,000 years ago when early farmers started eating plant-based diets and didn’t get as much vitamin D from fish and meat as hunter-gathers did. . . .“People that lived in Europe between 40,000 years ago and 8,000 years ago were as dark as people in Africa. . . .“We have always imagined that [Europeans] became light-skinned much faster. But now it seems that this happened actually quite late in human history.”
From Science News. The paper and its abstract are as follows:
The Tyrolean Iceman is known as one of the oldest human glacier mummies, directly dated to 3350–3120 calibrated BCE. A previously published low-coverage genome provided novel insights into European prehistory, despite high present-day DNA contamination. Here, we generate a high-coverage genome with low contamination (15.3×) to gain further insights into the genetic history and phenotype of this individual. Contrary to previous studies, we found no detectable Steppe-related ancestry in the Iceman. Instead, he retained the highest Anatolian-farmer-related ancestry among contemporaneous European populations, indicating a rather isolated Alpine population with limited gene flow from hunter-gatherer-ancestry-related populations. Phenotypic analysis revealed that the Iceman likely had darker skin than present-day Europeans and carried risk alleles associated with male-pattern baldness, type 2 diabetes, and obesity-related metabolic syndrome. These results corroborate phenotypic observations of the preserved mummified body, such as high pigmentation of his skin and the absence of hair on his head.
K. Wang et al. "High-coverage genome of the Tyrolean Iceman reveals unusually high Anatolian farmer ancestry." Cell Genomics (August 16, 2023). doi: 10.1016/j.xgen.2023.100377.
The open access paper states in the body text that:
We found that the Iceman derives 90% ± 2.5% ancestry from early Neolithic farmer populations when using Anatolia_N as the proxy for the early Neolithic-farmer-related ancestry and WHGs as the other ancestral component (Figure 3; Table S4). When testing with a 3-way admixture model including Steppe-related ancestry as the third source for the previously published and the high-coverage genome, we found that our high-coverage genome shows no Steppe-related ancestry (Table S5), in contrast to ancestry decomposition of the previously published Iceman genome. We conclude that the 7.5% Steppe-related ancestry previously estimated for the previously published Iceman genome is likely the result of modern human contamination. . . .
Compared with the Iceman, the analyzed contemporaneous European populations from Spain and Sardinia (Italy_Sardinia_C, Italy_Sardinia_N, Spain_MLN) show less early Neolithic-farmer-related ancestry, ranging from 27.2% to 86.9% (Figure 3A; Table S4). Even ancient Sardinian populations, who are located further south than the Iceman and are geographically separate from mainland Europe, derive no more than 85% ancestry from Anatolia_N (Figure 3; Table S4). The higher levels of hunter-gatherer ancestry in individuals from the 4th millennium BCE have been explained by an ongoing admixture between early farmers and hunter-gatherers in the Middle and Late Neolithic in various parts of Europe, including western Europe (Germany and France), central Europe, Iberia, and the Balkans.Only individuals from Italy_Broion_CA.SG found to the south of the Alps present similarly low hunter-gatherer ancestry as seen in the Iceman.We conclude that the Iceman and Italy_Broion_CA.SG might both be representatives of specific Chalcolithic groups carrying higher levels of early Neolithic-farmer-related ancestry than any other contemporaneous European group. This might indicate less gene flow from groups that are more admixed with hunter-gatherers or a smaller population size of hunter-gatherers in that region during the 5th and 4th millennium BCE. . . .
We estimated the admixture date between the early Neolithic-farmer-related (using Anatolia_N as proxy) and WHG-related ancestry sources using DATES to be 56 ± 21 generations before the Iceman’s death, which corresponds to 4880 ± 635 calibrated BCE assuming 29 years per generation (Figure 3B; Table S7) and considering the mean C14 date of this individual. Alternatively, using Germany_EN_LBK as the proxy for early Neolithic-farmer-related ancestry, we estimated the admixture date to be 40 ± 15 generations before his death (Table S7), or 4400 ± 432 calibrated BCE, overlapping with estimates from nearby Italy_Broion_CA.SG, who locate to the south of the Alps (Figure 3B).While compared with the admixture time between early Neolithic farmers and hunter-gatherers in other parts of southern Europe, for instance in Spain and southern Italy, we found that, particularly, the admixture with hunter-gatherers as seen in the Iceman and Italy_Broion_CA.SG is more recent (Figure 3B; Table S3), suggesting a potential longer survival of hunter-gatherer-related ancestry in this geographical region.
7 comments:
Press release at https://www.sciencedaily.com/releases/2023/08/230816114103.htm
The contemporary enthusiasm for getting away from whiteness, means that I am going to maintain some reservations about this work until I hear it assessed by independent researchers.
In particular, the part where they say, we didn't find any steppe DNA, so the original sample must have been contaminated, seems like a big sudden leap. What do the original team think of this? Are the new team saying that the contamination was contemporary, or could it have been historical? Is there any possibility that the steppe DNA is there, but the new team just failed to detect it?
Curly hair, bald, very dark skin.
"until I hear it assessed by independent researchers."
The claim that people in Europe were dark skinned in the Neolithic era and among hunter-gathers is long standing and is not new to the paper. Light skin color entered the modern European phenotype during the period of steppe admixture (although it was probably gradually getting lighter over time at higher latitudes). The quote about the skin color being as dark as Africans is less strong than it appears at face value, because of the great range of skin color within Africa (and even within sub-Saharan Africa), particularly at higher latitude regions, such as in the Sahel and in Ethiopia.
European Neanderthals were lighter skinned than the first modern humans in Europe, the Cro-Magnon hunter-gatherers. Light colored skin is not a trait that is believed to have been acquired through Neanderthal admixture, however.
We know from modern human genetic history that skin color is one of the more rapidly evolving phenotypes due to fitness based selection in relation to latitude as survival risks from sun burn and skin cancer balance themselves against risks from low levels of Vitamin D.
Blue eyes in Europeans are a Holocene era de novo mutation that happened just once in Northern Europe. The white skinned, blue eyed phenotype didn't exist in Europe until post-Last Glacial Maximum autochthonous Europeans admixed people with steppe ancestry.
"Is there any possibility that the steppe DNA is there, but the new team just failed to detect it?"
Virtually nil. The new team's measurement was much more precise and higher quality than the original one. Contamination is also a well known risk in ancient DNA studies that was a common problem in the earlier ancient DNA studies. As a result of those earlier missteps, methods to prevent contamination of ancient DNA samples have become the norm.
The fact that the steppe ancestry in the older study with a lower quality measurement of the Otzi ancient DNA was an outlier that was hard to explain otherwise also makes the contamination theory very plausible.
"We know from modern human genetic history that skin color is one of the more rapidly evolving phenotypes due to fitness based selection in relation to latitude as survival risks from sun burn and skin cancer balance themselves against risks from low levels of Vitamin D."
Lactose tolerance in Europeans also emerged at notable frequencies after steppe admixture, although it was rare in the Yamnaya steppe people as well and it isn't clear if this trait emerged de novo post-steppe migration in Northern Europe, or if it was already present at low frequencies in steppe people and rose to a high frequency in Northern Europe due to fitness based selection. I narrowly favor the latter hypothesis because in community graves in the Bronze Age, high steppe ancestry families usually had greater lactose tolerance rates than low steppe ancestry families. Lactose tolerance may not have been as fitness enhancing for light skinned herders on the Pontic Caspian steppe as it was for people now engaged in farming in Northern Europe.
The simultaneous combination of strong selective pressures on lactose tolerance and light skin suggests that Vitamin D was very important for selective fitness.
Vitamin D boosts the immune system (which is important to resist plagues which are also especially common during periods of famine which were more common in early agriculture with little long distance trade in bulk commodities like grain). Vitamin D deficiencies in women greatly reduce their fertility and greatly impair the survival chances of their infant children.
http://secher.bernard.free.fr/blog/index.php?post/2023/08/31/Le-g%C3%A9nome-%C3%A0-haute-couverture-d-%C3%96tzi
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