This is the third, and final post on MUC 19 (links to part 1 and part 2). Following the MUC19 gene inherited by Humans from Neanderthals, who in turn got it from Denisovans, led me to a paper by Peyrégne et al., 2020 which adds a very interesting piece of evidence about the introgression dates of Denisovans and Neanderthals into Americans, one that the authors find inconsistent with accepted theories (it is far too old!). In this post we will look into these very early dates.
When did Denisovans and Neanderthals Admix with Humans?
In Peyrégne et al., 2020 paper in the section Dating Denisovan gene flows into modern humans the authors "estimated Denisovan admixture times using the exponential decay of the linkage disequilibrium between alleles inherited from Denisovans in present-day individuals" What this means is that groups of genes that are close to others along a DNA strand tend to be inherited together, as a group, in a non-random manner (this is the definition of Linkage Desequilibrium) these chunks of genes imply a shared origin or inheritance, introgression. The "exponential decay" means that these connected genetic packets tend to decay, or break down over time (due to processes like recombination), across generations, following a mathematical rule, which follows an curve known as an exponential curve.
This enabled the researchers to "estimate Denisovan admixture times of 50-39ka in South Asians and 44-35ka in East Asians, approximately 20% and 29% more recent than Neandertal admixture time estimates in these populations (62-49ka – the range of estimates obtained for Eurasians), respectively." They displayed these results in the paper's Extended Figure 3 Estimation of Denisovan and Neandertal admixture dates and in Supplementary Note 11. Below you can see Figure 3. The introgression dates are given in generations. But since the paper states that generation time is 29 years, I converted the values to years in the table further down.
As you can see, for each Eurasian group and the Oceanians (Papuans), the Denisovan admixture generation number ranges from 937 to 1511 generations ago, but form the Mexican (Los Angeles) or MXL group the figure is 50% higher: 2097 generations. A similar effect can be seen in the Neanderthal introgression date for non-Americans it varies between 1070 and 1862 genertions, the MXL have a value of 2097 generations.
The caption acknowledges this incongruency and gives a vague explanation (excuse): "The estimate of the Neandertal admixture in Native Americans is inconsistent with estimates for all other groups. This seems to be driven by over-estimates of the recombination rates in the population-specific recombination maps perhaps due to the complex admixture history of Native Americans." Many words, but no beef!
Heading to Supplementary Note 11 on page 170, the authors write (highlighting is mine): "we re-analyzed the admixture linkage disequilibrium decay in the 1,000 Genomes populations... using the same ascertainment strategy described above while measuring genetic distance based on the respective recombination map available for each population. This yielded Neandertal admixture time estimates that are consistent with previous estimates, except for American populations where the estimates are older (Figure S100). This discrepancy likely represents uncertainties in inferring recombination rates in these admixed populations, as similar biases were observed when using the recombination map inferred in American populations to measure genetic distance in other populations. A similar trend was observed for the Denisovan admixture time, with estimates ranging between 1,146 and 1,705 generations ago (33ka-49ka) in most populations, and between 2,069 and 2,469 generations ago in American populations (Figure S100)."
Below is the Figure S100 mentioned above, I only show the data for Americans:
I prepared the following table with the data given by the authors and calcualted the date in years using the generation time of 29 years:
The Large Gap in Introgression Dates
Comparing the MXL individual with the Han Chinese, the Denisovan and Neanderthal introgression in the former took place 24 ky before the latter one!
The authors, in the supplementary material note some anomalies regarding the Native American groups: "We see that Native Americans exhibit lower match rates to Denisova 3 and Vindija 33.19 for both Denisovan-like and Neandertal-like segments, respectively, than other populations (except Oceanians, where some Denisovan segments may be misidentified as Neandertal segments; Figure S102 andFigure S103), suggesting a higher false positive rate in Native Americans (i.e. modern human ancestry misidentified as archaic ancestry)." Interestingly, Denisova 3 is a recent Denisovan, from Altai, and the Vindija individual is from Croatia, in Europe, so one would not expect them to be present in the American Natives who had already received the introgression of a different, and more diverse group of Denisovans and Neanderthals as their admixture was earlier than that of the other groups (Figures and table above).
The authors explain it away: "It is likely that the results for Native Americans are confounded by greater genetic drift between the allele frequencies of Native Americans and those of Africans used as reference for distinguishing archaic and modern human ancestry."
The other thing noted by the authors (highlight is mine) is that "Native Americans and West Eurasians include considerably lower match rates than observed in Oceanians and South Asians, these likely represent a larger proportion of false positives (i.e. Neandertal or modern human ancestry) among the few Denisovan-like segments identified in Native Americans and West Eurasians. Restricting the analysis to segments of 0.1cM or longer removes most segments with a low match rate to Denisova 3 in both populations, which is consistent with an increased false positive rate in these populations, while the results remain consistent for other populations (Figure S106). As the difference in match rates for Native Americans and West Eurasians compared to Denisova 25 and Denisova 3 are then only marginally significant (p>0.01), it remains unclear whether these two populations also carry a more divergent Denisovan ancestry."
The MUC19 gene in Americans came from a Denisovan closer to the older clade of Denisovans living in SE Asia, and is distant from the Denisova 3 individual. This could account for the "low match rate to Denisova 3", regarding Europeans, they have a very low Denisovan admixture, so it isn't surprising it comes from another source and not the distant Altai Denisova 3.
According to Villanea et al., the MUC19 gene supposedly "... was inherited by modern humans through introgression with a population closely related to the Chagyrskaya and Vindija Neanderthal" Considering these individuals lived, in Altai, Siberia, Asia, and Croatia, Europe, respectively, this statement can only refer to a population of West Asian Neanderthals.
Admixture and an early date for the peopling of America
Çonsidering this data, the best explanation for the dates and populations is the one I outlined in part 2 of this series: The Humans that eventually reached America, were part of the first population to enter Eurasia, and admixture with older Neanderthals ~100kya in the Caucasus region (Turkey, Georgia, Iran, Armenia, Irak) on the fringe area between non-Altaian Denisovans (the ones that introgressed with SE Asians and Papuans, and probably are the source of the Austronesian signal in Amerindians), and West Asian Neanderthals. They then headed into Central Siberia.
This is in line with Yuan K, et al., 2020, and the admixture they found in the remains from Ust'Ishim, Siberia, which are 45,000 years old (he predates the admixture times given by Peyrégne et al., 2020 for the Eurasian populations, suggesting his lineage received an earlier introgression (Yuan et al., point out that they "also detected two waves of Neanderthal-like introgression in the Ust’-Ishim genome: a recent one (1.41–1.57%) that occurred 61.4–57.8 kya and a weaker and more ancient one (0.04–0.20%) that occurred 204.1–95.6 kya."
It is likely that Ust'Ishim is just a sample, of a sub-population that remained behind, part of the people who moved across Siberia, far from the Altai Denisovans, heading North (possibly the 38 kya Yana people in Northern Siberia are another sub-population along the migration route towards America. A group of people who entered the New World around 35-40 kya.
Index to this series of posts on MUC19
Patagonian Monsters - Cryptozoology, Myths & legends in Patagonia Copyright 2009-2026 by Austin Whittall ©
No comments:
Post a Comment