Researchers Suggest 2 Neanderthals Present at Same Siberian Cave Were Distant Relatives

A recent article discusses the genetic analysis of a tiny bone fragment from Denisova Cave in Siberia's Altai Mountains (they propose it is 110,000-years-old) They suggest that it reveals that two Neanderthals who occupied the same site roughly 10,000 years apart were distant relatives. The bone, belonging to a male individual dubbed D17, yielded only the fourth high-quality Neanderthal genome sequenced to date. When compared with the other known Neanderthal genomes, they propose that it shows that the population in this remote region was small, isolated, and characterized by low genetic diversity long before Neanderthals went extinct around 34,000 years ago.

The study, published in PNAS, suggests how fragmented and vulnerable Neanderthal groups were, even in a cave that was intermittently shared with Denisovans over hundreds of thousands of years. They do not acknowledge that both Neanderthals and Denisovans were descendants of Noah, or that they were even human. Their analysis focuses on ages for these fragments, based on their genetic information. This is an excellent opportunity to look for any assumptions made in the analysis, and determine if there were biases or conflicts that resulted in data that at first glance seems to be in conflict with Biblical truth.

The method used in the study is molecular (genetic) clock dating based on DNA sequence data from the specimens themselves. 

Specifically, for the key ~110,000-year-old Neanderthal bone fragment (called D17 or Denisova 17) found in Denisova Cave (in the Altai Mountains of Siberia), researchers estimated the age by counting the number of transversion substitutions that had accumulated on the autosomes (non-sex chromosomes) since the last common ancestor with chimpanzees. This “branch shortening” approach in the nuclear genome produced an age estimate of ~110 thousand years (99–120 ka at 2 standard deviations). It was cross-checked against the mitochondrial genome (~132 ka, with a 95% high posterior density interval of 92–175 ka) and the Y chromosome (~120 ka, 95% HPDI 100–142 ka). Similar molecular-clock techniques (comparing derived alleles to modern reference genomes, calibrated against present-day African individuals) were used to assign ages to other Neanderthal and Denisovan specimens from the cave or comparative sites. Cave-layer chronology also draws on other methods like optically stimulated luminescence (OSL) and radiocarbon dating in broader studies, but the paper relies primarily on these genetic methods for the specific bone ages.

Nathaniel Jeanson’s discoveries (primarily his work on Y-chromosome and mitochondrial DNA mutation rates) highlight fundamental flaws in this approach, particularly its reliance on phylogenetic calibration and assumptions of deep time. Jeanson, a geneticist with Answers in Genesis, has shown through pedigree-based (direct, observed) mutation-rate studies that human Y-chromosome and mtDNA diversity accumulates far faster than the slow “phylogenetic” rates used in standard molecular clocks. Those phylogenetic rates are typically calibrated against assumed ancient fossil divergences (e.g., human-chimp split millions of years ago), creating circular reasoning: the method assumes old ages to derive a slow rate, then uses that rate to “prove” old ages. Jeanson’s data compress the timeline dramatically—human Y-chromosome TMRCA and global genetic diversity fit within a biblical ~6,000-year framework (post-Flood ~4,500 years ago) when using the faster, empirically measured rates and a Noah-rooted tree.

Applied to the Denisova Neanderthal genomes:

• The transversion-substitution clock (and the mtDNA/Y clocks used for consistency) inherits the same circular calibration problem. Jeanson’s models predict far less accumulated variation than observed if the specimens were truly 110 ka old; conversely, the observed variation fits recent post-Flood diversification when the clock is properly calibrated to direct mutation rates and population-growth curves.

• Jeanson has explicitly tested Neanderthal Y-chromosome data as a case study for ancient-DNA validity. Including it disrupts the tight match between his Y-chromosome mutation accumulation and historical population-growth records under a young-earth model; excluding it (or re-rooting the tree to a post-Flood Noah lineage) restores the fit. He therefore treats such ancient sequences as either contaminated, miscalibrated, or requiring reinterpretation rather than accepting the deep-time ages they imply.

• Broader young-earth critiques note that molecular clocks ignore potential post-Flood environmental effects on mutation rates, incomplete lineage sorting, and the fact that Neanderthal/Denisovan DNA can be placed on a Ham-lineage branch descending from Noah in creationist re-analyses—again only if the deep-time ages are rejected.

  
  

In short, the genetic-dating method used in the article assumes evolutionary deep time for its rate calibration, while empirically grounded, pedigree-calibrated clocks demonstrate that the same data are far more consistent with a recent origin for the variation observed in these Neanderthal genomes. This is why he and related researchers view the 110 ka (and similar) age assignments as inflated and unreliable.

This is typical of the bias present in much of the work being done in the fields of human origins and genetics.