Why Neanderthal Mothers Left No Mitochondrial Trace Today

Here is the puzzle. Modern people carry Neanderthal DNA in our chromosomes, typically about 1.8–2.6% in Europeans and a bit higher in East Asians, with roughly 20% of the Neanderthal genome surviving in aggregate. Yet not a single living human mitochondrial lineage is Neanderthal.

All the Neanderthal we keep is nuclear, not maternal: 0% of living human mtDNA lineages are Neanderthal, despite widespread nuclear ancestry. (reference)

This absence has been read as a verdict on fertility, social dominance, even prehistoric romance. The better answer is more prosaic, and more interesting. It is about how lineages persist or vanish, how small populations buckle under demography, and how a few early encounters set the terms for everything that followed.

Absence of Neanderthal mtDNA does not mean hybrids were sterile. It means that no Neanderthal-mother lineage persisted in an unbroken chain of daughters to the present. That can happen for many reasons that have nothing to do with biology: chance, famine, a run of sons, or a daughter who has no children. Nuclear DNA, which shuffles every generation, preserves ancestry more broadly, which is why Neanderthal segments dot our genomes while their mtDNA does not.

There is also a strong signal that interbreeding was sex biased. Several studies find less Neanderthal ancestry on the X chromosome than on autosomes, consistent with more matings between Neanderthal males and modern human females and with some purifying selection against archaic variants on the X. See summaries in this review of Neanderthal genetics and recent analyses of X-chromosome patterns in PLOS Genetics.

The last major pulses of Neanderthal-to-human gene flow likely occurred about 65–47 thousand years ago, inferred from segment lengths and linkage patterns. (overview)

So mtDNA alone cannot tell us whether Neanderthal–human matings “worked.” A spectacular case from Siberia answers that directly: a first-generation child of a Neanderthal mother and a Denisovan father, sequenced from a tiny bone fragment. Hybrids were viable and, at least sometimes, fertile. The genome is described in Nature.

• Sex-biased contact and social structure. Encounters that left descendants were more often Neanderthal men with modern human women, not the reverse. That pattern matches the X-chromosome signal and would funnel surviving mtDNA toward modern-human types. Social dynamics matter here. A child typically grows up in the mother’s group. If most mixed unions were modern-human mothers with Neanderthal fathers, the children’s mtDNA was modern from the start, and their descendants remained within modern-human networks.
• Demography and drift. Neanderthals lived in small, scattered populations for hundreds of thousands of years, with low genetic diversity and frequent inbreeding. In such settings, even common lineages wink out by chance. A handful of Neanderthal-maternal lines could have entered modern populations, but over millennia they could easily have been lost in a much larger, expanding human population. Genetic drift is relentless. As the ancients say, lineages die in silence.
• Selection against some archaic mtDNA. Mitochondria power every cell, and their genes interact tightly with nuclear genes. Mismatches can be costly. Several teams have proposed that some Neanderthal mtDNA or Y lineages were purged by selection, while many neutral or adaptive nuclear segments persisted. This idea is difficult to prove definitively, but it fits broader patterns of negative selection against Neanderthal variants that affected fitness in modern humans, summarized in multiple genomic studies.

These forces are not mutually exclusive, and the data support some of each. The important corrective is this: no one needs to invoke universal hybrid sterility. The archaeological and genetic record show successful matings across archaic groups, followed by a long period in which some lineages thrived while others faded.

Across all living humans, about 20% of the Neanderthal genome survives in pieces, even though each person carries only a few percent. (overview)

A 2020 study in Science analyzed Neanderthal and Denisovan Y chromosomes and found that Neanderthals’ Y lineages had been replaced by modern-human–related Y chromosomes hundreds of thousands of years ago. Mitochondrial genomes tell a similar story: Neanderthal mtDNA also shows signs of ancient introgression from a modern-human–like population some 219–413 thousand years ago, summarized in the genetic literature collated here.

In other words, there was a quiet genetic coup inside Neanderthal populations long before the well-known later interbreeding that left traces in us. These early exchanges likely reflect the same forces, in reverse: small Neanderthal effective population sizes, drift, and selection favoring some incoming lineages that worked better with existing nuclear backgrounds.

This reframes the modern absence of Neanderthal mtDNA. It is not a unique indictment of Neanderthal mothers or of hybrid fertility. It is what repeated pulses of contact, sex bias, demography, and selection do to uniparental markers over deep time. They are winners-take-all lineages. Most lose.

So what should we actually infer? The weight of evidence suggests that modern humans and Neanderthals met many times, sometimes had children, and that those unions tended to involve modern-human mothers. Their nuclear genes persist in us in small but meaningful ways, sometimes with adaptive effects on immunity and metabolism. Their maternal lines do not, because uniparental lineages are fragile and history is long.

If anything, the more striking observation is that Neanderthals were already absorbing modern-human maternal and paternal lines long before we absorbed theirs. The boundary between “them” and “us” was porous for a very long time.

• More ancient DNA from early modern humans in the Levant and Arabia, the most likely zones for early contacts that reshaped Neanderthal mtDNA and Y chromosomes.
• Functional tests of ancient mtDNA and nuclear compatibility, which could clarify how selection shaped uniparental lineage survival.
• Denser sampling of late Neanderthal groups, to map where, and how recently, modern-human–related mtDNA and Y chromosomes took over.