View Full Version : Mystery genes – do we have an unknown extinct ancestor?

rock hunter
07-29-2016, 11:19 PM
Mystery genes – do we have an unknown extinct ancestor?

NEW RESEARCH HAS discovered populations from South and Southeast Asia contain a small amount of ancestral DNA – not present in East Asians or Europeans – suggesting some modern humans have another, mystery ancestor.

The research – undertaken by Professor Jaume Bertranpetit from Pompeu Fabra University in Spain along with a team of researchers and published in Nature Genetics this week – involved whole-genome sequence analysis.

The genome sequences of 60 individuals of different ethnicities from India’s mainland were compared with those of 10 Andamanese individuals as well as publicly available data for other populations.

Unknown, extinct ancestor
The study found a small proportion of the genome sequence in populations from South and South East Asia contained DNA from an unknown, extinct, hominid ancestor.

Dr Alan Cooper, from the University of Adelaide and Australian Centre for Ancient DNA, said at least five ancestral hominids had been present in Southeast Asia – including Neanderthals, Denisovians, Homo floresiensis ('hobbits'), H. erectus and H. antecessor.

“We already knew there was another species or group of hominids in Southeast Asia who had contributed to the Denisovan genome,” commented Alan, who wasn't involved in this study.

“This paper further confirms that one other group, maybe the same one, has contributed to modern humans.”

This is not the first time ancestral DNA has been found in modern humans – when Homo sapiens (that's us) arrived in Southeast Asia about 60,000 years ago, they shared the space with the now extinct Denisovians – and today, Melanesians carry 4% of this ancestral DNA.

There is speculation over the mystery ancestor, with Alan suggesting Homo erectus (“upright man”) or an Asian Homo antecessor (“human pioneer”) as potential hominid groups of interest.

"A crowded stage"
However, without a well preserved specimen – the preservation process is hindered by Asia’s hot and humid climate – Alan said it will be difficult to determine the exact source of the genomic sequence.

“At the moment there’s not any good skeletal remains that are likely to provide DNA,” Alan said.

For now, the genetic information that is available can help scientists piece together what the ancestor potentially looked like.

“At the moment we are able to see the genetic shadow left behind in other genomes, but we’re not sure what fossils it is connected to," Alan said.

However, it could also be from a previously unidentified ancestral hominid. “I wouldn’t be surprised,” he added.

“What we can say safely is that Asia was a far more crowded stage.”


07-30-2016, 09:30 PM
Red boxes represent extinct non-African hominins who introgressed into modern humans; these introgressions are marked with dotted lines. Green boxes represent populations that may have admixed with the new unknown hominin.

To shed light on the peopling of South Asia and the origins of the morphological adaptations found there, we analyzed whole-genome sequences from 10 Andamanese individuals and compared them with sequences for 60 individuals from mainland Indian populations with different ethnic histories and with publicly available data from other populations. We show that all Asian and Pacific populations share a single origin and expansion out of Africa, contradicting an earlier proposal of two independent waves of migration1, 2, 3, 4. We also show that populations from South and Southeast Asia harbor a small proportion of ancestry from an unknown extinct hominin, and this ancestry is absent from Europeans and East Asians. The footprints of adaptive selection in the genomes of the Andamanese show that the characteristic distinctive phenotypes of this population (including very short stature) do not reflect an ancient African origin but instead result from strong natural selection on genes related to human body size.

An unknown extinct hominin could be Java Man (Homo erectus erectus) or its related species such as Solo Man which was also discovered in Java. Aboriginal Australians and Melanesians carry 4-6% of Denisovan DNA and Denisovans who migrated to Melanesia may have interbred with the likes of Java Man, leaving their genetic footprints on modern-day Melanesians. Modern humans interbred with Denisovans around 45,000 years ago in Papua New Guinea but Denisovans and Java Man had coexisted in the region prior to the arrival of modern humans for hundreds of thousands of years. Approximately 1% of Denisovan DNA looks much older than the remaining 99%, which shows that the Denisovans interbred with another early hominin species (Lachance et al. 2012; Hammer et al. 2011).

Although it is likely that this 1% of Denisovan mtDNA came from another ancient hominin, it is also possible that it — or some of it — came from some species of ancient bacteria — microbes that routinely exchange DNA with their environments (such as the human gut microbiome, which functionally impacts our immune systems) and with other bacteria and other microbes. There is some decent evidence that at least some of our DNA (perhaps mostly non-coding, “transposable” DNA) got there via some ancient infectious pathogen (but in a hominin line long extinct). Although, whether such an infection, or series of infections, could introduce 1% of a species’ DNA (and then be positively selected and passed on) is debatable.