On human and Neanderthal - Denisovan mtDNA

There is no evidence at all of extant Neanderthal mtDNA in modern humans. This seems quite surprising, and many explanations have been offered. But the most simple and clear cut one is, in my opinion, the lack of enough samples of Neanderthal mtDNA tested to date. And this is precisely what this paper says: No Evidence of Neandertal mtDNA Contribution to Early Modern Humans, by David Serre, Andre Langaney, Mario Chech, Maria Teschler-Nicola, Maja Paunovic, Philippe Mennecier, Michael Hofreiter, Göran Possnert, Svante Pääbo (Published: March 16, 2004https://doi.org/10.1371/journal.pbio.0020057)

They clearly state the following:

"..Under the model of a constant human effective population size (Tavare 1984; Nordborg 1998) of 10,000 over time (Figure 4A), any contribution of Neandertal mtDNA to modern humans 30,000 years ago larger than 25% can be excluded at the 5% level (Figure S3). A more realistic scenario may be that the spread of modern humans was accompanied by an increase in population size before and during their migration out of Africa and subsequent colonization of western Eurasia (see Figure 4B). In that case, the Neandertal contribution that can be excluded is smaller (i.e., less gene flow could have taken place)...
It is noteworthy that under the model of constant population size, about 50 early modern human remains would need to be studied to exclude a Neandertal mtDNA contribution of 10%. To exclude a 5% contribution, one would need to study more early modern human remains than have been discovered to date. Thus, definitive knowledge of the extent of a putative contribution of Neandertals to the modern human gene pool will not be possible... ."

The authors indicate that the Neandertal fossil remains carry "closely related mtDNAs that are not found among current humans", in fact all reads are very similar to each other and, different to the standard modern human reference.

They mention the possible causes for this lack of Neanderthal mtDNA in H sapiens: "...such a contribution might have been erased by genetic drift or by the continuous influx of modern human DNA into the Neandertal gene pool. A further concern is that if some Neandertals carried mtDNA sequences similar to contemporaneous humans, such sequences may be erroneously regarded as modern contaminations when retrieved from fossils.".

Both causes seem very reasonable and the authors fin that this "... excludes any large genetic contribution by Neandertals to early modern humans, but does not rule out the possibility of a smaller contribution."

So, after all, there may have been a small introgression of Neanderthal mtDNA into us.

An intersting point to ponder is that "Although mitochondria retain their own genome, the vast majority of the >1000 proteins that function in mitochondria are encoded in the nucleus" (from The Mitonuclear Dimension of Neanderthal and Denisovan Ancestry in Modern Human Genomes. Joel Sharbrough Justin C. Havird Gregory R. Noe Jessica M. Warren Daniel B. Sloan. Genome Biology and Evolution, Volume 9, Issue 6, 1 June 2017, Pages 1567–1581, https://doi.org/10.1093/gbe/evx114).

This means that the mitochondrial genes and the nuclear genes that encode these proteins (known as N-mt genes), proteins used by the mitochondria, have to adapt to each other during episodes of introgression in order to function correctly and not cause the death of the hybrid individual.

Sharbrough et al then apply this concept to Neanderthal ⁄ Denisovan admixture with H. sapiens:

"The potential for mitonuclear interactions among hominins is of interest because, unlike in the nuclear genome, there has not been any detectable mtDNA introgression from Neanderthals or Denisovans into modern human populations (Krings et al. 1997; Serre et al. 2004). Regardless of what has caused this lack of mtDNA introgression, one consequence is that all introgressed Neanderthal and Denisovan nuclear alleles must function on a modern-human mitochondrial background..."

In other words if there is no Neanderthal or Denisovan mtDNA in humans, our modern mtDNA however must have had to adapt to the N-mt genes that did introgress from our older relatives (Neanderthals and Denisovans). And their paper looks into this.

They concluded that "... genes involved in mitochondrial function may have been subject to distinct selection pressures during the history of introgression from archaic hominins but that mitonuclear incompatibilities have had, at most, a small role in shaping genome-wide introgression patterns, perhaps because of limited functional divergence in mtDNA and interacting nuclear genes."

In other words there wasn't much incompatibility between the mtDNA and the N-mt genes after all! And this was because our and their mtDNA and nuclear genes were, or are, very similar. Which is what you'd expect anyway, we all branched off from the same tree not that long ago (say 750 Ky).

I do look forward to mtDNA sequences more complete in nature, from more individuals (archaic H. sapiens and Neanderthal & Denisovans), who knows, we may actually find one with a shared mtDNA Haplogroup...

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