Although it was published last June, a paper by Hsieh et al, is very interesting, and worthy of a post (free access to it her: A global map for introgressed structural variation and selection in humans. bioRxiv [Preprint]. 2025 Jun 24:2025.06.24.661368. doi: 10.1101/2025.06.24.661368. PMID: 40667000; PMCID: PMC12262424). It is not peer-reviewed so its conclusions should be taken with caution.
The paper looks into the introgression of archaics into modern people in Papua New Guinea and I highlight the following findings:
It Adds diversity
The authors state that "some archaic sequences likely contributed to human phenotypic variation" and that they were not necessarily bad for us (deleterious as other papers have suggested). Instead the paper proposes that "many introgressed loci in our genome show signatures of positive selection." They go on to add that Structural Variants or SVs, "such as insertions, deletions, and inversions, contribute disproportionately to human genetic diversity by affecting more genomic sequences than SNVs."
Denisovan and Neanderthal admixture in PNG
The authors noticed that "Unexpectedly, PNG individuals carry more Neanderthal sequences than Denisovan, contradicting the expected genome-wide estimates of ∼4% Denisovan and ∼2% Neanderthal ancestry" This is surprising, and they try to explain it as follows: "[caused by the differences between the sequenced Denisovan genome and the actual Denisovan population that interbred with the ancestors of the PNG as well as complex demographic histories in Oceania." Translated: We don't know why this happened!
MUC19
They observed the presence of a rare introgressed SV, the MUC19 segment: "... an introgressed variable number tandem repeat (VNTR) haplotype at the MUC19 locus with an uncertain archaic origin." I posted about MUC19 last March, because it is supposedly enriched among Amerindians, giving them adaptative advantages, and it is believed to have originated in Denisovans, and passed on to humans via Nenaderthals. These people in PNG have the variant. So it is not so uncommon as believed.
The timing of the introgression
The authors estimate that one of the SV introgressions, an insertion in chromosome 16 "diverged from the others about 596 thousand years ago (kya; range: 322–870 kya)" which is a rather wide range! and attribute it to Denisovans and that the actual "admixing" between Denisovans and the ancestors of the PNG people took place between 60 and 170 kya. Which is older than you would expect and consistent, in my opinion, with an early out of Africa event, or, perhaps a non-African modern human group mixing with Denisovans 170,000 years ago.
Centromeres
If you imagine a chromosome pair with its characteristic "✘" shape, the centromere is the place where the chromosome arms narrow down and meet. Since humans are diploid, we have 23 pairs of chromosomes (each with one paternal and one maternal chromosome) with a total of 46 individual chromosomes. Each chromosome of the pair links with the other one to form the typical "X" shape: "❱" to the left, and "❰" to the right join at the centromere (located at the apex of each single chromosome).
During cellular division (which I will oversimplify in this description) the cell sends fibers that attach to the centromere and and pulls the chromosomes apart, half going to one side, the other half going to the opposite side of the dividing cell. So centromeres play an important role in regulating the division of cells, and reproduction, where the sexual cells carry half the chromosome load compared to regular ones.
The paper goes on to look into centromeres, and reports that it found "11 centromeres likely derived from archaic hominins" and looks into them in detail.
The authors state, for instance, that the PNG people carry a centromere lineage (haplotype 2 chromosome 4) that is older than those found in other modern humans: "[it] diverged from the rest of the modern human lineages 489,447 – 507,131 years ago... also observed evidence for archaic origins for the chromosome 22 centromeres... The lineage that gave rise to the[m] ... diverged from other modern human lineages approximately 580,661 years ago (95% HPD interval: 469–694 kya... sugesting that these centromeres are likely introgressed from archaic hominins into the early ancestors of the PNG."
African divergence and superarchaic introgressions
An earlier paper by Langley et al., 2019 aldo studied the centromere region (they call them Cenhaps, large-scale haplotypes that span the centromere-proximal regions or CPRs in chromosomes). They reported that they found that Africans carry a very ancient, basal, diverged variant of a centromere not found outside of Africa in humans, and it predates the split of Neanderthal-Denisovans from the Modern human branch. The authors find that non-Africans carry another varaint closer to Neanderthals than Denisovans (proof of the admixture of OOA humans with Neanderthals). The superarchaic admixture in Africans comes from a 1.1 million-year-old hominin, and happened recently. The full text is the following:
"The most diverged, basal clade in the chr12 CPR is common in Africa, but, like the most diverged chrX cenhap, is not represented among the descendants of the out-of-Africa migrations (Bae et al., 2017). The great depth of the lineage of this cenhap is further supported by comparison to homologous archaic sequences (Green et al., 2010; Prüfer et al., 2014; Prüfer et al., 2017). 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 Figure 3b). This putatively archaic chr12 cenhap represents a large and obvious example of the potentially introgressed sequences within African populations inferred from model-based analyses of the distributions of sequence divergence (Hammer et al., 2011; Hsieh et al., 2016; Durvasula and Sankararaman, 2019). The small out-of-Africa cenhap nested within a mostly African subclade appears to be a typical Eurasian archaic introgression with higher affinity to Neanderthals (DM/(DN + DM)=0.91 and DM/(DM +AN)=0.90) than to Denisovans (Figure 3b). This bolsters the conclusion that the basal African cenhap represents a distinctly older 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 (Prüfer et al., 2017). While there is no direct evidence of recent introgression, the large genomic scale of the most diverged chr12 cenhap (relative to apparent exchanges in other cenhaps) is consistent with recent admixture with an extinct archaic in Africa
... Two examples are chromosome 8, containing an ancient cenhap limited to Africa with an estimated TMRCA of ~730 KYA, and chr10 that appears to harbor another clear Neanderthal cenhap introgression..."
Again, and this time from another source, we see proof of ancient surviving archaic hominins in Africa mating with Africans, recently, and in the process, adding to their diversity and divergence.
Patagonian Monsters - Cryptozoology, Myths & legends in Patagonia Copyright 2009-2026 by Austin Whittall ©
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