Earlier this week, I introduced the concept of relictation, the mathematically derived fixation of ancestral variation through population bottlenecks, as a third distinct mechanism of genomic change alongside natural selection and genetic drift. Relictation was proposed to account for patterns of divergence that neither selection nor drift could explain within the available timelines, as demonstrated by the MITTENS accounting framework.
MITTENS performs an all-cause accounting of genomic divergence. It counts every base pair of difference between two complete, gap-free genomes and compares the total against the empirically observed rate at which changes become fixed in real populations. The result, across every great ape species examined, is that the observed divergence considerably exceeds what fixation can produce in the available time, by multiple orders of magnitude.
Relictation offered a partial answer to the observed accounting problem. If speciation events involve small founding populations carrying non-representative samples of ancestral variation, the resulting lineages would show divergence patterns that look like accumulated substitutions but are actually inherited differences, relics of the ancestral population’s diversity, established across the entire species in one stroke by the bottleneck itself. I looked into that by utilizing Unauthorized’s twin 96-core 512GB RAM beasts to analyze all six complete ape genomes provided by the T2T Primate Consortium. Analysis of the fine-grained distribution of substitutions across the human genome now suggests that relictation cannot be the whole story and may not be the only discrete mechanism at work.
The substitution density across the genome is massively overdispersed, more than 80 times more variable than a uniform-rate process predicts. This variation is not random. Dense regions cluster next to other dense regions, forming contiguous blocks of elevated substitution with sharp boundaries in a pattern we call mesas. Within these mesas, the substitutions are disproportionately concentrated on the human lineage. A single mesa on a single chromosome shows an excess of human-lineage substitutions that exceeds both the MITTENS fixation ceiling and the maximum that natural selection can theoretically fix across the entire genome according to Haldane.
These mesa signatures are consistent with relictation. A bottleneck could produce exactly this shape. But the sheer scale and density of the mesas raises an inescapable question: is there too much structured divergence for multiple bottleneck events to credibly account for?
So I am now contemplating whether what the mesas reveal is a fourth mechanism operating alongside relictation, or an alternative third mechanism that produces the same signature through a different cause. I propose the term sigillation for the hypothesis that some of these mesa regions represent deliberate genomic modification: discrete engineering events that wrote contiguous blocks of change into one dominate lineage. Sigillation predicts the same observable shape as relictation, featuring elevated density, sharp boundaries, and lineage asymmetry, but from a fundamentally different cause.
Both hypotheses remain open. And both may be true simultaneously, as some mesas may be bottleneck relics while others are indications of genetic engineering. Distinguishing between them will require significant further research by those with the tools to do so. But what the data establish beyond any dispute is that a) the mesa signature exists, b) that it is the dominant source of genomic divergence between humans and the great apes, and, c) no account of speciation is complete without it.
Sigillation is no more proof of IGM than relictation is. But it may be initial evidence of IGM. I stress that sigillation is not the only possible explanation for the observed anomalies; the evidence also credibly points to far more outlandish hypotheses than mere intelligent engineering being performed on this planet at some point in the past. What we do know is that neither natural selection nor neutral diffusive drift can still be considered viable candidates. And there is no need to take my word for anything with regards to this, all of the data has been provided by the T2T Primate Consortium (Yoo et al. 2025) aligned with Progressive Cactus (Armstrong et al. 2020).
