Sunday, 26 August 2018

Hybrid Hominins! An individual with a Neanderthal mother and a Denisovan father

A letter [1] published 22nd August 2018 in Nature reports on the discovery of a bone fragment from a young female hominin whose mother was Neanderthal and whose father was Denisovan. That hybridisation between hominin species occurred in the past is no longer in question, but this discovery provides evidence of a first-generation cross between two different hominins, something which in itself is remarkable. Studies like this are no longer necessary to falsify creationist assertions about human origins as the evidence against universal human descent from two people living six thousand years ago is overwhelming, but to have evidence of a first-generation cross between two different hominin groups further underscores how human origins is far more amazing and complicated than the special creationist can imagine.

The bone fragment in question comes from Denisova cave, located in the Altai mountans in Siberia, Russia. Denisova cave gives its name to the Denisova hominins, identified from DNA from a number of bone fragments found in it. While we don't have anything near a complete skeleton of any Denisovan, genomic analysis shows that they share a common ancestor with Neanderthals, with estimates of their divergence time around  430,000 years ago. [2]

Prior to the discovery of this fragment, we already knew that after the Homo sapiens / Homo neanderthalensis lineages, and the Denisovan / Neanderthal lines diverged, there had been interbreeding between the separate lineages. Family trees [3] aren't quite as neat as one would imagine.

Source - Reference 3

What we didn't have was evidence of first-generation interbreeding, namely a hominin whose parents were from different lineages. Admittedly, no one was expecting that given both the odds of finding fossils in the first place with preserved DNA and finding an individual from the first generation of such interbreeding, but as the 2018 paper shows, this is exactly what  has been found.

Genetic analysis of the bone fragment, known as Denisova 11, shows that it is female, while bone thickness suggests the female was around 13 years old. It's believed to have lived around 90,000 years ago.

Genetic analysis of Denisova 11 shows that it had roughly equal Denisovan and Neanderthal DNA. Two possible explanations for this are that Denisova 11 came from a population of hominins carrying roughly equal proportions of Neanderthal and Denisovan DNA, or that Denisova 11 was the product of Neanderthal and Denisovan parents. Genetic analysis carried out by the authors showed that the latter was the case. Denisova 11 had a Neanderthal mother and a Denisovan father.

Percentage of sites at which two sampled DNA fragments both carry Neanderthal-like alleles (NN, blue), Denisovan-like alleles (DD, red), or one allele of each type (ND, purple); and the expectations for an offspring of a Neanderthal and a Denisovan (F1), of two F1 parents (F2), and of an F1 and a Denisovan (F1×D). Source: Figure 2 of reference 1 (including caption text).
The discovery is one that is anything other than a footnote in population genetics and palaeoanthropology:
The results convincingly demonstrate that the specimen is indeed a first-generation hybrid, says Kelley Harris, a population geneticist at the University of Washington in Seattle who has studied hybridization between early humans and Neanderthals. [Population geneticist Pontus] Skoglund agrees: “It’s a really clear-cut case,” he says. “I think it’s going to go into the textbooks right away.” [4]
The analysis also showed that Denisova 11's father also had Neanderthal ancestry in his past, further illustrating the interbreeding that occurred between human lineages after divergence:
Relationships and gene flow events between Neanderthal and Denisovan populations inferred from genome sequences. Diamonds indicate ages of specimens estimated via branch shortening; circles indicate population split times estimated from allele sharing between Denisova 11 and the high-coverage Neanderthal and Denisovan genomes (blue and red) and among the three high-coverage genomes (yellow, from a previous publication). Markers indicate the means of these estimates, error bars indicate 95% confidence intervals based on block jackknife resampling across the genome (n = 523 blocks). Note that the confidence intervals do not take the uncertainty with respect to population size, mutation rates or generation times into account. Ages before present are based on a human–chimpanzee divergence of 13 million years. The arrow indicates Neanderthal gene flow into Denisovans. Source: Reference 1 (including caption text).

Studies such as this are important in shedding light on the timing and details of human evolution, and show that the once-incredible concept of sequencing genomes of fossils hundreds of thousands of years old is finally allowing old bones to talk.

Speak to the earth and it will teach you - Job 12:8


1. Slon, V. et al. "The genome of the offspring of a Neanderthal mother and a Denisovan father"   Nature (2018)
2. Meyer, M. et al. "Nuclear DNA sequences from the Middle Pleistocene Sima de los Huesos hominins." Nature (2016) 531:504–507
3. Warren M "Mum's a Neanderthal, Dad's a Denisovan: First discovery of an ancient-human hybrid." Nature 22nd August 2018
4. ibid