New Insights into Human Origins - Part 2

Kia ora,

I have previously mentioned on this blog that the study of human origins is a keen interest area of mine. So, with the recent publication of a couple of relevant research papers, I couldn't resist the opportunity to come back to the topic!

The papers in question are on the subject of the Denisovans - an enigmatic group of hominins presently known only from a few very fragmentary fossils recovered from sites in Siberia (Denisova Cave, after which they are named) and on the Tibetan Plateau. These fossils are so fragmentary in fact that no physical description of the Denisovans exists and they have yet to be given a proper species classification like Homo sapiens (the classification of our own species). The presence of hominins distinct from both Homo sapiens and Neanderthals (Homo neanderthalensis) at Denisova Cave, in the Altai Mountains in southern Siberia, ca. 50,000 - 30,000 years ago was brought to light thanks to the sequencing of genetic material (DNA) extracted from a tiny finger bone (Denisova 3) found at the cave in 2008. 

Replica of the Denisovan finger bone fragment found at Denisova Cave in 2008, on display at the Museum of Natural Sciences in Brussels, Belgium.
Image: Thilo Parg / Wikimedia Commons (CC BY-SA 3.0)

Further work at Denisova Cave suggests that Denisovans first visited the cave at least 200,000 years ago, and possibly as far back as 300,000 years ago. Neanderthals are also known to have visited the cave; the discovery at the site of a fragment of a hominin long bone (Denisova 11) with the genetic signature of a first generation Neanderthal-Denisovan offspring confirmed that the two groups of hominins must have met and interbred. Comparison of Denisovan DNA with DNA from present-day humans indicates that groups of Homo sapiens and Denisovans also met and interbred, possibly on multiple occasions, with the genetic legacy of such interactions evident in present-day Melanesian and East Asian populations.

The presence of Denisovan DNA in these present-day populations strongly suggests in itself that Denisovan populations were not restricted solely to southern Siberia. The only Denisovan fossil recovered from a site other than Denisova Cave to date is a partial mandible (lower jawbone) found in 1980 by a Buddhist monk in Baishiya Karst Cave on the Tibetan Plateau (at 3,280 metres above sea level). No DNA was preserved in the mandible, so the Denisovan identification was based on ancient proteins extracted from a sample of the dentine from an attached molar tooth. (I have discussed the use of ancient protein sequences as an alternative to ancient DNA for the study of hominin phylogenies, or evolutionary relationships, in a previous post on this blog). Despite uncertainty about exactly where in the cave the mandible had come from, a sample of matrix adhering to the fossil was able to be dated to at least 160,000 years old.

Although this mandible is at present the only known Denisovan fossil from a site other than Denisova Cave there are other Asian hominin fossils of uncertain taxonomy that experts have suggested could also be Denisovan.  

Denisovan mandible from Baishiya Karst Cave.
Image: Dongju Zhang / Wikimedia Commons (CC BY-SA 4.0)

The first of the recent papers reports on further work at Baishiya Karst Cave. The presence of Denisovans at the site over an extended period of time has now been confirmed by the recovery of Denisovan mitochondrial DNA from excavated sediments deposited approximately 100,000 and 60,000 years ago, and possibly as recently as 45,000 years ago. It is also reported in the paper that stone artefacts and animal bone fragments were recovered from throughout the excavated deposits, which are thought to have started accumulating around 190,000 years ago. Together with the date associated with the mandible (>160,000 years old), the available evidence points to a long occupation of the Tibetan Plateau by the Denisovans, during which it is likely that they became well adapted to the high altitude environment. As suggested by other researchers, the genetic adaptations to high altitudes in present-day Tibetans could have been inherited from Denisovans. This is a possibility that would become all the more likely if the presence of Denisovans in the area 45,000 years ago, close to the time that Homo sapiens are believed to have reached this part of the world (by 40,000-30,000 years ago), is able to be confirmed. 

The second paper reports the presence of Denisovan DNA in the genomes of two early East Asian Homo sapiens fossils. The first is a newly sequenced genome from an approximately 34,000 year old skull cap discovered in the Salkhit Valley of northeastern Mongolia. The second is a previously sequenced genome from an approximately 40,000 year old individual from Tianyuan Cave in the Beijing area in China. Interestingly, both of these individuals carried segments of Denisovan DNA that are also found in present-day populations across mainland East Asia, but not in present-day Melanesian populations, despite the later populations carrying around twenty times as much Denisovan DNA. This finding provides direct evidence from ancient genomes to support previous suggestions that groups of Homo sapiens and Denisovans met and interbred on multiple occasions, which until now had been based on comparisons of Denisovan DNA with DNA from present-day humans.

Thanks for reading,

Nick