Modern humans interbred with Neanderthals 100,000 years ago

Ancient DNA from Altai Neanderthal female is first evidence of modern human contribution to Neanderthal genome

Ever since the first draft of the Neanderthal genome was published in 2010, it has been known that Neanderthals interbred with modern humans and it is now believed that around twenty percent of their genome survives in the present-day population. Subsequent work revealed the existence of a new human species in the Russian Altai, the Denisovans, and that parts of their genome also survive in the present-day population. It has also been established that the Altai Denisovans also interbred with Neanderthals in the region and with another as yet unidentified archaic species (probably Homo erectus). What has hitherto been absent up is evidence of gene flow from early modern humans into archaic genomes.

To address this issue, researchers investigated the previously-sequenced genome of a Neanderthal woman who lived in the Altai region 50,000 years ago. They found evidence of gene flow from modern humans into the ancestors of the Altai Neanderthal. The source was unclear, but was thought to be a modern population that either split from the ancestors of all present-day Africans, or was one of the early modern African lineages. It was estimated that the implied interbreeding occurred at least 100,000 years ago – well before the previously-reported gene flow from Neanderthals into modern humans outside Africa 47,000 to 65,000 years ago. However, they did not find evidence for similar gene flow from modern humans into either Denisovans or European Neanderthals.

The traditional view that modern humans did not leave Africa and the Levantine/Arabian region until around 60,000 years ago has been refuted by the discovery of teeth lying within the modern range at Fuyan Cave, China, dating to around 100,000 years ago. If modern humans were in China then it is entirely possible that they were also in the Altai at that time. Other possibilities are the Arabian Peninsula, where there is archaeological (though no fossil) evidence for a modern human presence as long ago as 127,000 years ago and Neanderthals were likely to also have been present; and the Levant where there is fossil evidence for both Neanderthals (Tabun) and modern humans (Skhul and Qafzeh) 120,000 to 110,000 years ago.

Kuhlwilm, M. et al., Ancient gene flow from early modern humans into Eastern Neanderthals. Nature, doi:10.1038/nature16544 (2015).




Flores ‘hobbits’ arose from an archaic human species

Study confirms that Flores hominins are not Homo sapiens  

Since their headline-making discovery in 2003, the diminutive hominins from the Indonesian island of Flores have been generally accepted to be a distinctive human species, Homo floresiensis. Popularly referred to as ‘hobbits’, they are widely believed that they owe their small size to a phenomenon known as ‘insular dwarfism’. In the absence of dangerous predators and in a habitat where food is scarce, it was suggested that they ‘downsized’ from their ancestral condition as evolution favoured smaller, less ‘gas-guzzling’ individuals. The ancestral species is often claimed to be Homo erectus, but claims have also been made for more primitive hominins such as Homo habilis or even Australopithecus.

Not everybody accepted that Homo floresiensis was a new human species and among the sceptics was the late Teuku Jacob, an Indonesian anthropologist who claimed that the ‘hobbits’ were modern humans affected by a developmental disorder known as microcephaly. Some years after Jacob’s death, his former colleagues revived the theory, this time claiming that Homo floresiensis were modern humans suffering from Down syndrome.

A newly-published study describes the investigation of the cranial bones of the partial female skeleton LB 1 (popularly and perhaps inevitably known as ‘Flo’). A series of high-resolution scans were taken using an X-ray CT scanner. Comparative scans were also taken of microcephalic specimens used in earlier studies of LB 1. The scans were used to study the bone thickness distribution of the cranial vault and internal bone composition and structure. Cranial vault thickness (CVT) can be diagnostic of a hominin species attribution, and it was found to be thick for LB 1 in absolute terms and even more so in relative terms when the small cranial size is taken into account. By contrast, microcephalic skulls of modern humans are thinner than those of humans unaffected by the condition. It was found that Flo had suffered from a condition known as bilateral hyperostosis frontalis interna, and bore the healed scar of a head injury, but there was nothing to indicate that she had suffered from any developmental disorders of the type suggested by Jacob or his former colleagues.

The researchers showed that LB 1 displays characteristics related to the distribution of bone thickness and arrangements of cranial structures that are primitive traits for hominins, differing from the derived condition of modern humans. This was not seen with the microcephalic skulls.

The study thus rules out the possibility that LB 1 can be assigned to Homo sapiens, but leaves the issue of its true affinities unresolved.

Balzeau, A. & Charlier, P., What do cranial bones of LB1 tell us about Homo floresiensis? Journal of Human Evolution 93, 12-24 (2016).

Adverse effects of interbreeding with Neanderthals

Not all ‘imported’ genes were beneficial
Interbreeding with Neanderthals and Denisovans is believed to have introduced many beneficial genes into the modern genome, helping the immune systems of early modern humans to fight pathogens to which they had not previously been exposed. Other ‘imported’ genes include those involved with the production of keratin, a protein that is used in skin, hair and nails, and in East Asian populations, many genes involved with protection from the sun’s UV rays are of Neanderthal origin. It is likely that the transfer of these genes helped early modern humans to adapt to conditions away from their African homeland.

However, a newly-published study suggests that interbreeding with Neanderthals also had a down side. Researchers analysed the electronic health records (EHR) of 28,000 individuals of European origin and integrated the data with high resolution maps of Neanderthal haplotypes across individual modern human genomes. They carried out a large-scale assessment of the functional effects of DNA inherited from Neanderthals on health-related traits in these individuals. Particular use was made of genotype and phenotype data from the Electronic Medical Records and Genomics Network, which is a consortium that links EHR systems combined with patient genetic data from nine sites across the USA.

Genes of Neanderthal origin were found to be associated with smoking addiction, increased risk of depression, incontinence, bladder pain, urinary tract disorders, protein calorie malnutrition, and actinic keratosis (precancerous skin lesions resulting from exposure to the sun). One gene variant was associated with blood coagulation, increasing the risk of strokes. These results follow on from earlier work which implicated increased risk of Crohn’s disease and type 2 diabetes with Neanderthal genes.

Many of these genes would have been advantageous to Neanderthals: for example, the benefits of enhanced blood coagulation would have greatly outweighed the risk of strokes when injuries leading to significant loss of blood were a part of daily life and few people lived past forty. In other cases, genes were probably once advantageous but adverse effects were triggered by the changes in diet following the coming of agriculture in Neolithic times.

Depression can be triggered by disturbed circadian rhythms. It is possible that Neanderthal brain chemistry and skin responses to sunlight were both linked to the lighting conditions and lifestyles of an era when artificial light consisted of torches and camp fires. In which case, the genes might only have become maladaptive with the advent of widespread artificial lighting.

The methodology used by the researchers is likely to provide further insight into the genetic impact of these ancient encounters between Neanderthals and modern humans.

Simonti, C. et al., The phenotypic legacy of admixture between modern humans and Neandertals. Science 351 (6274), 737-741 (2016).


Milner Hall yields first hominin fossils

Fossils recovered at ‘Cradle of Humankind’ site

Sterkfontein is a set of limestone caves near Krugersdorp, South Africa. It is one of the most important hominin fossil-bearing sites in the world and finds include the female australopithecine Mrs Ples, discovered in 1947 and recently voted No.95 in a list of 100 Great South Africans. Sterkfontein has yielded stone tools in addition to hominin fossils and it is now part of the Cradle of Humankind, a World Heritage Site named by UNESCO in 1999. Most of the finds have been made in Members 4 and 5 of the cave’s sedimentary sequence, but rather less well known is the large underground chamber known as Milner Hall.

It is from Milner Hall that the discovery is reported of a hominin adult upper right molar (M1) tooth and a proximal phalanx finger bone, probably from a left hand. The chamber has previously yielded only stone tools, and association with these suggests that the fossils are 2.18 million years old.

The tooth is broadly closer to Homo than to Australopithecus or Paranthropus. It most closely resembles the Olduvai OH 6 first molar assigned to Homo habilis and a first molar assigned to the recently-proposed Homo naledi. The shape and size of the tooth’s cusps align it to early Homo.

The finger bone is larger and more robust than that of any hominin so far discovered in South Africa. It resembles the Olduvai Homo habilis fossil OH 7, but is much larger. It is markedly curved, within the range of Australopithecus afarensis and suggesting adaptation for tree-climbing, but it lacks other features associated with arborealism, such as a strongly developed flexor apparatus and a mediolaterally expanded diaphysis; these features are present in A. afarensis, Homo habilis and present-day chimpanzees. The finger bone possesses an enigmatic mixture of primitive, derived and unique characteristics. It is not clear whether or not it belonged to the same individual and its taxonomic affinities are at this stage uncertain.


Stratford, D., Heaton, J., Pickering, T., Caruana, M. & Shadrach, K., First hominin fossils from Milner Hall, Sterkfontein, South Africa. Journal of Human Evolution 91, 167-173 (2016).