400,000 Year Old Hominid Genome Sequenced


Another hominin genome, another spanner in the works for hominid evolutionary scholars.

Thanks to the continuing rapid development and improvement of sequencing technologies a team of researchers have been able to sequence the mitochondrial genome from the femur of a 400,000 year old hominid in a cave in Spain called Sima de los Huesos, eerily translated to Pit of Bones. The site is well known for it’s ancient archeological finds.

Sequencing ancient DNA is no easy task, DNA breaks down over time and samples become contaminated with animal and human sequences, but as technology continues to advance, so does our capability to sequence more and more complex samples. Mitochondrial genomes are the most abundant due to the fact that every mitochondria carries it’s own copy of the mitochondrial genome and each cell has many mitochondria, which act as the energy factory of the cell. Even with the abundance of mitochondrial genomes in tissue it still took 2 grams worth of bone sample in order to sequence this latest genome.

With so much contamination and degradation you may be wondering how it is possible to sequence such old DNA. The trick is to break the sequences up into many smaller fragments and then piece them back together again where the genetic code overlaps. By using only the sequences that show a chemical characteristic of aging called cytosine deamination the amount of contamination is greatly reduced.

After all of that work the researchers were in for quite a surprise, the bones at Sima de los Huesos seem to carry Neanderthal derived features, especially in the facial region suggesting the species would share a common ancestor with the Neanderthals. This wasn’t the case however, using phylogenetic analysis, which assesses the commonality and divergence between genomes, the researchers discovered that the mitochondrial DNA seems to share a common ancestor with the Denisovan species which was discovered in Siberia, thousands of kilometers away. What’s more the Denisovan specimens are quite different morphologically to that of Neanderthals.

The very nature of mitochondrial DNA means that it is hard to accurately interpret exactly what this new discovery means in the grand scheme of the evolutionary tree of the hominin genus. Mitochondrial DNA unlike the DNA in the nucleus is not a combination of the genomes of the paternal and maternal lines. Instead it is passed down exclusively through the mother via the very first cell of a new organism, the fertilised ovum. This means that lines of mitochondrial DNA can appear and disappear over evolutionary time. In fact it is thought that during a population squeeze of early humans in Africa, only a single mitochondrial genome survived, the so called “ancestral Eve”.

The authors of the paper propose several explanations for the new results, the first is that this new species is genuinely closely related to the Denisovans, however this hypothesis is difficult to maintain when considering the fact that Denisovans must have covered a much larger geographical area than previously thought, as well as existing along side the Neanderthals. This would raise the question of how the two groups could occupy such similar environments yet still be so different on a genetic level. What’s more the specimen at Sima de los Huesos most likely pre-dates the time the Neanderthals and Denisovans split by at least 100,000 years.

Another explanation is that the Sima de los Huesos hominin might be related to a population of homins that later became an ancestor to both the Neanderthals and the Denisovans, although the problem of how the mitochondrial DNA of both groups later became so different would also need to be explained. Perhaps this sequence later went extinct in Neanderthals and was replaced by a new mitochondrial lineage, much like the ancestral eve scenario.

Perhaps the most plausible explanation is that a completely distinct group of hominids introduced this mitochondrial line to both the Sima de los Huesos hominins and the Denisovans through interbreeding. Recent evidence is increasingly suggesting that inbreeding was much more common between different hominid species than was classically assumed.

It will be almost impossible to know for sure until much more informative nuclear DNA (or full genome) sample can be analysed. Unfortunately nuclear DNA is much harder to obtain due to the fact only one copy per cell is present which means you need much larger samples.

What this new data shows is that classical ideas of hominid and indeed human evolution has been too constrained by ideas of human privilege and such a dire shortage of samples with which to draw conclusions, as technology improves and more nuclear DNA is sequenced, who know what we may learn about ourselves and our ancestors?



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