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: https://doi.org/10.1101/351569).
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).
The finding is interesting, and it supports the idea of an enhanced modern African diversity due to the archaic admixture event with modern Africans.
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