Correlated and geographically predictable Neanderthal and Denisovan legacies are difficult to reconcile with a simple model based on inter-breeding - William Amos June2021.
Abstract –
Although the presence of archaic hominin legacies in humans is taken for granted, little attention has been given as to how the data fit with how humans colonized the world. Here, I show that Neanderthal and Denisovan legacies are strongly correlated and that inferred legacy size, like heterozygosity, exhibits a strong correlation with distance from Africa. Simulations confirm that, once created, legacy size is extremely stable: it may reduce through admixture with lower legacy populations but cannot increase significantly through neutral drift. Consequently, populations carrying the highest legacies are likely to be those whose ancestors inter-bred most with archaics. However, the populations with the highest legacies are globally scattered and are unified, not by having origins within the known Neanderthal range, but instead by living in locations that lie furthest from Africa. Furthermore, the Simons Genome Diversity Project data reveal two distinct correlations between Neanderthal and Denisovan legacies, one that ***starts in North Africa ***and increases west to east across Eurasia and into some parts of Oceania, and **a second, much steeper trend that starts in Africa**, peaking with the San and Ju/’hoansi and which, if extrapolated, predicts the large inferred legacies of both archaics found in Oceania/Australia. Similar ‘double’ trends are observed for the introgression statistic f4 in a second large dataset published by Qin and Stoneking (Qin & Stoneking 2015 Mol. Biol. Evol. 32, 2665–2674 (doi:10.1093/molbev/msv141)). These trends appear at odds with simple models of how introgression occurred though more complicated patterns of introgression could potentially generate better fits. Moreover, substituting archaic genomes with those of great apes yields similar but biologically impossible signals of introgression, suggesting that the signals these metrics capture arise within humans and are largely independent of the test group. Interestingly, the data do appear to fit a speculative model in which the loss of diversity that occurred when humans moved further from Africa created a gradient in heterozygosity that in turn progressively reduced mutation rate such that populations furthest from Africa have diverged less from our common ancestor and hence from the archaics. In this light, the two distinct trends could be interpreted in terms of two ‘out of Africa’ events, an early one ending in Oceania and Australia and a later one that colonized Eurasia and the Americas..
[ 22. June 2021, 01:26 PM: Message edited by: the lioness, ]
-------------------- Without data you are just another person with an opinion - Deming Posts: 12143 | From: When you have eliminated the impossible, whatever remains, however improbable | Registered: Jun 2007
| IP: Logged |
posted
I said this so many times. I just love being right. Here this study has confirmed what I have been saying all along. It is impossible for Neanderthal and AMH to …do the nasty and have babies. It only in the mind of Paabo and his buddies that would come up with such a hypothesis. Animals and human hybrid. This is where they want to take us. “ Sweet tooth”. Nevertheless, It points to an AMH origin of the so called Neanderthal and Denisovan genetic markers. So can we stop the nonsense of humans and Neanderthal fugkinh and having babies. Furthermore it points to a North African and even Khoi-San origin of the genes.
What did I tell you? Hublin et al has North Africa being occupied for the last 200,000 years. Was it Tishkoff or Henn also speculated of a North African origin of AMH?
[ 22. June 2021, 01:24 PM: Message edited by: the lioness, ]
-------------------- Without data you are just another person with an opinion - Deming Posts: 12143 | From: When you have eliminated the impossible, whatever remains, however improbable | Registered: Jun 2007
| IP: Logged |
posted
“Despite a high level of general acceptance, the idea archaic legacies are near-ubiquitous in humans is not without issue. As yet, convincingly “archaic mitochondrial DNA, X chromosomes or Y chromosomes have yet to be found in humans”. While this absence might be the result of purifying selection, this implies that hybrid individuals would have appreciably reduced fitness, presenting a barrier to gene flow. More directly, hybridization since the out of Africa event around 70 000 years ago [29] would result in legacies where most introgressed fragments are rare and hence heterozygous. I have tested this prediction by using a form of conditioned D where sites are excluded/included depending on whether they are heterozygous/homozygous in one of the two humans being compared [30].I found that the excess base sharing between non-Africans and archaics captured by D is driven almost entirely by heterozygous sites in Africa acting to increase African–Neanderthal divergence rather than introgressed fragments in non-Africans acting to decrease non-African–Neanderthal divergence: the exact opposite of what is expected under the classical inter-breeding hypothesis.”
“One way to help distinguish between introgression and mutation rate variation as mechanisms capable of causing variation in levels of base sharing between different human populations and archaics may be to examine the extent to which different legacies are correlated. The introgression model predicts that legacies will tend to reflect where and when inter-breeding occurred. For example, the large peak of inferred Denisovan legacy in Papuans [4,23,26] and much lower levels elsewhere suggests that inter-breeding with Denisovans occurred mainly in East Asia/Oceania. Equally, the ubiquity of the inferred Neanderthal legacy is difficult to explain unless most inter-breeding occurred in the Levant [3,38], soon after humans migrated out of Africa. The two legacies are, therefore, expected to be un- or even negatively correlated. By contrast, if inferred legacies are artefacts linked to global variation in human mutation rate, the two legacies should tend to covary. Here, I test predictions from these two competing hypotheses through analysis of the 1000 genomes data, through a ****reanalysis ***of two large published studies and through coalescent simulations. Specifically, I ask: (i) whether signals of introgression for the two archaics are correlated, as expected under mutation slowdown, or show appreciable independence, as expected if inter-breeding between the two archaics occurred at different geographical locations”
-------------------- Without data you are just another person with an opinion - Deming Posts: 12143 | From: When you have eliminated the impossible, whatever remains, however improbable | Registered: Jun 2007
| IP: Logged |
posted
So here the author is stating how Paabo cooked up the data to discard the African component.
quote:
“is unusual in the way it seeks to minimize overlap between signals of introgression due to Neanderthal and those due to Denisovans, but at the same time, it suffers from an inherent bias. . By conditioning on a panel of sub-Saharan Africans not carrying the derived archaic allele, it effectively **prejudges** the idea that archaic introgression into Africa never occurred and also, potentially, underestimates introgression into populations that are most closely related to Africans, particularly wherever there is any appreciable gene flow. This is because derived archaic variants found in the African panel will be automatically excluded. In reality, recent studies suggest introgression did occur into Africans [25,28]. Moreover, by focusing only on transversions, approximately two-thirds of the data are being discarded. Consequently, I decided to explore alternative versions of ndNEA, with and without conditioning on the African state and comparing the uses of transitions with that of transversions."
[ 21. June 2021, 12:38 PM: Message edited by: the lioness, ]
-------------------- Without data you are just another person with an opinion - Deming Posts: 12143 | From: When you have eliminated the impossible, whatever remains, however improbable | Registered: Jun 2007
| IP: Logged |
quote:Originally posted by xyyman: I said this so many times. I just love being right. Here this study has confirmed what I have been saying all along. It is impossible for Neanderthal and AMH to …do the nasty and have babies. It only in the perverted mind of Paabo and his ambi-sexual buddies that would come up with such a hypothesis. Animals and human hybrid. This is where they want to take us. “ Sweet tooth”. Nevertheless, It points to an AMH origin of the so called Neanderthal and Denisovan genetic markers. So can we stop the nonsense of humans and Neanderthal fugkinh and having babies. Furthermore it points to a North African and even Khoi-San origin of the genes.
What did I tell you? Hublin et al has North Africa being occupied for the last 200,000 years. Was it Tishkoff or Henn also speculated of a North African origin of AMH?
posted
The problem is there are so many lies and spin going on. Not only in politics but also in genetic studies. The Covid-19 situation has opened my eyes more. There are organizations in place controlling not only what we see and what we hear but what we read in scientific journals. Their supposed Covid-19 crisis has exposed them. It is a cluster-fugkh. Lol!.
Going to the 7th Sixers game Sunday night gave a clearer example of how they feed us BS on TV. Mask was required to enter the Arena. As soon as people entered the Arena they discarded their mask. About 95% 40,000 unmasked fans(except 1-or-2), rubbing shoulders and screaming at the game. But the TV mostly showed masked individuals.
I have come to the realization that we need more independent (of Max Planck and Paabo/Reich) and impartial researcher. It doesn’t make much sense reading many papers now because they parrot the same bs and narrative. It is old. Occasionally someone breaks rank. Like this paper and challenges Paabo. But they are sometime stifled.
The only recourse is more independent researchers and a website where they can publish.
-------------------- Without data you are just another person with an opinion - Deming Posts: 12143 | From: When you have eliminated the impossible, whatever remains, however improbable | Registered: Jun 2007
| IP: Logged |
posted
I wouldn't get my hopes up just yet. They have now just found a new "human ancestor".
quote: CELL PRESS—A near-perfectly preserved ancient human fossil known as the Harbin cranium sits in the Geoscience Museum in Hebei GEO University. The largest of known Homo skulls, scientists now say this skull represents a newly discovered human species named Homo longi or “Dragon Man.” Their findings, appearing in three papers publishing June 25 in the journal The Innovation, suggest that the Homo longi lineage may be our closest relatives—and has the potential to reshape our understanding of human evolution.
UBBFriend: Email this page to someone!
Printer-friendly view of this topic