Guide to Patagonia's Monsters & Mysterious beings

I have written a book on this intriguing subject which has just been published.
In this blog I will post excerpts and other interesting texts on this fascinating subject.

Austin Whittall

Sunday, June 23, 2019

Archaic humans admixed with modern humans in Africa

News published on the Internet these last few days mentioned that scientists had discovered large strands of ancient DNA (i.e. Neanderthal and other even older archaic hominin) lurking in the "Dark Heart" of the human genome. I was intrigued after reading these laymen articles.

But the news is old, the original publication dates back to July 30, 2018, almost 11 months ago ( Haplotypes spanning centromeric regions reveal persistence of large blocks of archaic DNA, Sasha A. Langley, Karen Miga, Gary Karpen, Charles H. Langley, doi:

Their paper is interesting; they looked into "centromeres", specialized portions of DNA located more or less in the middle of chromosomes, that bind or link the two arms that text books typically show as a chromosome: one is the original chromosome, the other is its copy, they are called "sister chromatids" and form an "X" shaped structure. The centromer is where each part meets the other, in the "waist" of the "X".

Centromers serve to anchor fibers that pull the arms apart again when the cells divide, so each cell has one and only one chromosome.

The paper by Langley et al, reports "large-scale haplotypes (cenhaps) in humans" spanning the centromer region with "surprisingly deep diversity, including entire introgressed Neanderthal centromeres and equally ancient lineages among Africans".

They found that "Despite being fairly common among Africans today, a distinctly diverged chrX cenhap (cenhap 1, highlighted in purple, Fig. 1b,c) is rare outside of Africa. Examination of the haplotypic clustering (...) yields a parallel relationship among the three major cenhaps and an estimated Time of the Most Recent Common Ancestor (TMRCA) of ≈700 KYA (Fig. 1d) for this most diverged example.".

What is interesting is that they wonder about this very diverged cenhap: "It is unclear if this cenhap represents an introgression from a distinct archaic hominin in Africa or a surviving ancient lineage within the population that gave rise to AMHs". The ancient hominin admixing with modern humans is something that we have mentioned in other posts as a reason for the "greater diversity" of humans in Africa: they got a dose of very ancient DNA which increased their diversity, but this took place recently.

The paper states that it is old, but (as we highlighted in bold) it is consistent with a recent admixture:

"The most diverged, basal clade on chr12 (Fig. 2c, indicated in brown) is common in Africa, but, like the most diverged chrX cenhap, is not represented among the descendants of the out-ofAfrica migrations (26). The great depth of the lineage of this cenhap is further supported by comparison to homologous archaic sequences (21,22,23).
Consistent with the hypothesis that this branch split off before that of Neanderthals/Denisovans, members of this cenhap share fewer matches with derived SNPs on the Neanderthal and Denisovan lineages (DM) and exhibit strikingly more ancestral non-matches (AN) than other chr12 cenhaps (see Fig. 2b).
This putatively archaic chr12 cenhap represents a large and obvious example of the genome-wide introgressions into African populations inferred from model-based analyses of the distributions of sequence divergence (16,17).
(...) This bolsters the conclusion that the basal African cenhap represents a distinct, older and likely introgressed archaic lineage.
Unfortunately, there are too few coding bases in this region to support confident estimation of the TMRCAs of these ancient chr12 cenhaps. Based on the numbers of SNPs underlying the cenhaps, this basal cenhap is twice as diverged as the apparent introgressed Neanderthal cenhap, placing the TMRCA at ~1.1 MYA, assuming the Neanderthal TMRCA was 575KYA(23). While there is no direct evidence of recent introgression, the large genomic scale of this most diverged cenhap (relative to apparent exchanges in other cenhaps) is consistent with recent admixture with an extinct archaic in Africa, although, again, suppression of crossing over is an alternative explanation.

The finding is interesting, and it supports the idea of an enhanced modern African diversity due to the archaic admixture event with modern Africans.

Patagonian Monsters - Cryptozoology, Myths & legends in Patagonia Copyright 2009-2014 by Austin Whittall © 

Saturday, June 15, 2019

Ancestors of Neanderthal and Denisovans admixed with H. erectus

The paper published by Alan R. Rogers, Nathan S. Harris and Alan A. Achenbach (Neanderthal-Denisovan ancestors interbred with a distantly-related hominin June 14, 2019 finds evidence to support three human migrations out of Africa, the first one took place 1.9 Million years ago. The second wave happened 700,000 years ago and involved the ancestors of the Nenderthals and Denisovans (which they call "neandersovans". The last wave was that of modern humans. The oldest migration into Eurasia resulted in a population which they call "superarchaic".

They add: "..the large effective size of the superarchaic population hints that it comprised at least two deeply-divided subpopulations, of which one mixed with neandersovans and another with Denisovans."

They mention their molecular clock, which provided a date (95% confidence interval) of 1.9 to 2.5 Million years ago for the split between "superarhcaic" and the other trunk of mankind.

And coment that: "The lower end of this interval hardly differs from the 1.85 mya date of the earliest Eurasian archaeological remains at Dmanisi. It is possible that superarchaics separated from an African population 1.9 mya, expanded into Eurasia, and left those remains at Dmanisi. If so, then superarchaics descend from the earliest human dispersal into Eurasia. On the other hand, some authors prefer a higher mutation rate of 0.5 × 10−9 per year. Under this clock, the lower end of our confidence interval would be 1.7 mya. Thus, our results are also consistent with the view that superarchaics entered Eurasia after the earliest remains at Dmanisi."

They also find that the molecular clock calibrations used to calculate a Denisovan - Neanderthal split some 381,000 years ago by M. Meyer, et al., (Nature 531, 504, 2016) are too recent. They calculate the date of the split was almost twice that figure: 731,000 years ago.

This older date is in line with the 750 kya that we mention in our post Neanderthal and Denisovans split around 750 Kya (May 11, 2018), citing a paper by Ryan J. Bohlender and Chad D. Huff.

Although the paper does not name them, it is possible that the unknown super-archaic hominin population was in fact Homo erectus; they appeared around 2 million years ago which coincides with the split date between superarchaics and the other hominins calculated by Rogers et al.

This is in line with something we posted back in Dec. 2013 (Denisovans interbred with Homo Erectus), when we commented on a paper by Prüfer et al., that hinted at interbreeding between Denisovans and H. erectus.

Mendez, F. L., Watkins, J. C., Hammer, M. F., 2012. Global genetic variation at OAS1 provides evidence of archaic admixture in Melanesian populations. Molecular Biology and Evolution 29 (6),1513–1520.) also suggested an ancient admixture event between Denisovans and H. erectus: "These observations present the intriguing possibility that this deeply diverged region of OAS1 may have introgressed into the common ancestor of Denisova and Melanesians via admixture with an unsampled hominin group, such as Homo erectus. In fact, the introgression of a more archaic form into the ancestors of Denisova was also considered by Reich et al. (2010) to explain some archaic morphological features of the Denisova molar."


Patagonian Monsters - Cryptozoology, Myths & legends in Patagonia Copyright 2009-2014 by Austin Whittall © 
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Copyright © 2009-2018 by Austin Victor Whittall.
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