Scientists Find a Mysterious 'Ghost Lineage' In the DNA of West Africans
Researchers find evidence that a group of still-unknown humans interbred with our ancestors.
By Charles ChoiFebruary 14, 2020 10:15 PM
Ghost Lineage Ancestors - Shutterstock
(Credit: Zacarias Pereira da Mata/Shutterstock)

(Inside Science) — A mysterious extinct "ghost" human lineage that was an even more distant relation than Neanderthals may have interbred with the ancestors of modern West Africans, significantly contributing to their gene pool, a new study finds.

Although modern humans are now the only surviving lineage of humanity, others once lived on Earth. Some made their way out of Africa before we did, including the familiar Neanderthals in Eurasia and the newfound Denisovan lineages in Asia and Oceania. It isn't completely clear whether these lineages would be considered species or subspecies, but the groups had identifiable genetic differences. Prior work estimated the ancestors of modern humans split about 700,000 years ago from the lineage that gave rise to Neanderthals and Denisovans, and the ancestors of Neanderthals and Denisovans diverged from one another about 400,000 years ago.

The story is a bit more tangled than the timeline suggests, as genetic analysis of fossils of these extinct lineages has revealed they once interbred with modern humans, unions that may have endowed our lineage with helpful mutations as we began expanding across the world about 194,000 years ago. Neanderthal DNA makes up roughly 1.8% to 2.6% of the genomes of modern humans from outside Africa, whereas Denisovan DNA makes up 4% to 6% of modern Melanesians.


Read more: A Genetic Ghost Hunt: What Ancient Humans Live On In Our DNA?

Any number of now-extinct human lineages that once existed within Africa may have hybridized with modern humans there as well. However, the sparse nature of the ancient human fossil record in Africa makes it difficult to identify DNA from such "ghost lineages" in modern humans.

Instead of hunting for ancient human fossils across Africa, the scientists looked for genetic traces of ghost lineages in modern Africans. They compared 405 genomes from modern people from West Africa with ones from fossils of Neanderthals and Denisovans, focusing on DNA that stood out from the West African genomes roughly as much as Neanderthal and Denisovan DNA did from modern human genomes overall.

The researchers detected statistical anomalies they suggested were best explained by interbreeding between West Africans and an unknown ancient human lineage whose ancestors diverged from those of modern humans before the split between Neanderthals and modern humans. Four West African groups — Yoruba in southwestern Nigeria, Esan in southern Nigeria, Gambians in western Gambia, and Mende in Sierra Leone — may derive 2% to 19% of their DNA from a ghost lineage, the researchers said.

"Interbreeding among highly diverged human populations has been common through human evolution," said study senior author Sriram Sankararaman, a computational geneticist at UCLA.


A number of ghost lineage genetic variants were unusually common in the Yoruba and Mende genomes, suggesting they might confer some evolutionary advantages. These included genes involved in tumor suppression, male reproduction and hormone regulation.

Previous research also hinted at interbreeding with ghost lineages in Africa, such as a 2011 study examining sub-Saharan Africa and a January paper investigating western Central Africa. The ghost lineage examined in the January study "is likely the ghost lineage we are seeing," Sankararaman said. "A broader question of the number of these ghost lineages that have survived into present-day Africans is fascinating, which we don't have the answers to."

These findings underscore how "it is not a question of whether our ancestors interacted with other hominins, but it is a question of when, where, who," said evolutionary genomicist Omer Gokcumen at the University at Buffalo in New York, who did not take part in this research. "I think we will need additional ancient genomes from Africa to more properly address these questions."

The scientists estimated this ghost lineage diverged from the ancestors of Neanderthals and modern humans up to 1.02 million years ago and interbred with the ancestors of modern West Africans from 124,000 years ago up to the present day. "One limitation of our study is that we have mainly sampled present-day West African populations," Sankararaman said. They don't know yet how far the ghost lineage spread across Africa, he said.

The scientists aim to analyze people across Africa for signs of ghost lineages. "We are beginning to understand some of the complexities of human history, but the true picture is almost certainly even more complicated," Sankararaman said.


The researchers detailed their findings online Feb. 12 in the journal Science Advances.

This article originally appeared in Inside Science. Read the original here.

I posted this story I found from a science page. I don't know why it was titled this way, ghost could mean unknown origin. The truth is that even the Bible stated in Genesis 6 that some sons of God came and inter married with daughters of men and gave birth to giants and exceptionally advanced children which I presume continued today. The story is worth reading and let's have fruitful discussion as all these Ogiso , Eri and Oduduwa coming from the sky may be true, may be it was actually space ship or they were spiritual people . If history were to be believed then there could have been some descents from other planets whether angels or other being but stating that they were limited to any particular race may be deliberate as I believe that could have cut across all races which may include many so called geniuses as part of their descendants and I have thought privately that Orunmila, who invented the binary model called Ifa may have been a genius or a spiritual person but the factual Yoruba history are largely hidden in the algorithm of such spiritual corpus.

I just want knowledgeable people to make some meaningful contributions please

400,000 years ago is a lot and probably before Adam going by biblical records. My theory. This lineage could be a result of generation after generation of spiritism practice where disembodied being mix with humans.

I think the saying that IFE is where creation starts from, is about to get foothold!

Nonsense. They have found particles of Covid19 in some DNA.

Africans should be issued heavenly passports as we too often had contacts with the super naturals.

CodeTemplar:
400,000 years ago is a lot and probably before Adam going by biblical records. My theory. This lineage could be a result of generation after generation of spiritism practice where disembodied being mix with humans.

The Bible told this story in Genesis 6 as part of the early narratives of God's relationship with man. Whether it falls within the Biblical historical context or not, God acknowledged this event happened and new DNA emerged on earth, the Bible called them mighty men of old men of renown Genesis 6:4. The word those days and afterward caught my attention which could mean prior and later meaning such could still be alive today.
While the practice of spiritism can transform the spirit of a man I cannot say if it can transform his DNA, the blood especially.

romenna:
Africans should be issued heavenly passports as we too often had contacts with the super naturals.

I believe such contact may have happened across different cultures. The fact that such DNA variants were found and labelled as unknown or ghost could also mean that those stories of oduduwa, ogiso and may be Eri may be true as per people coming to earth with some kind of space ship or whatever. The truth is that we are always in contact with the supernatural through a form of spiritual relationships whether for good or otherwise.

orisa37:
Nonsense. They have found particles of Covid19 in some DNA.

The world is still discovering many things and even with the challenge of those interpreting the data found to favor whatever narratives that suit them, I think its now becoming clear that African stories may not be folklore after all

Ahmeduana:
I think the saying that IFE is where creation starts from, is about to get foothold!

Yes, that could have been true through the worldview of those concerns as there could have been many IFE in history. wE MUST SAY THAT THIS LED CREDENCE TO THE MANY MIGRATION STORY in many African societies.

MOD please move this story to politics section. it is an eye opening one that need contribution from all

Yeah I watched a similar documentary about the hormones or genes of Africans transformed from homosapience to humans and they were changed by —oh I forgot their name.

There could be a large amount of truth in it because have heard some stories as well about a particular town in Yoruba where some large amount of trees were turned to humans...

Some other stories where humans were made from a thing just for the purpose of mass farming.

Where do we categorize babies gotten from the gods, where do those babies come from and where are they presently?

What about those Iwins, Oro’s and egbere that exists in our stories then, where are those things now in our modern world?

If the truth could be found, it would explain a lot of things...

I hope I have this strand oo. Anything to separate me from average Nigerians is welcome to me right now.

Africans should be issued heavenly passports as we too often had contacts with the super naturals.

mandarin:
I posted this story I found from a science page. I don't know why it was titled this way, ghost could mean unknown origin. The truth is that even the Bible stated in Genesis 6 that some sons of God came and inter married with daughters of men and gave birth to giants and exceptionally advanced children which I presume continued today. The story is worth reading and let's have fruitful discussion as all these Ogiso , Eri and Oduduwa coming from the sky may be true, may be it was actually space ship or they were spiritual people . If history were to be believed then there could have been some descents from other planets whether angels or other being but stating that they were limited to any particular race may be deliberate as I believe that could have cut across all races which may include many so called geniuses as part of their descendants and I have thought privately that Orunmila, who invented the binary model called Ifa may have been a genius or a spiritual person but the factual Yoruba history are largely hidden in the algorithm of such spiritual corpus.

I just want knowledgeable people to make some meaningful contributions please

I think the pattern of the Yoruba, Igbo and Edoid groups talking of an ancestor coming from the sky has the same cultural origin.
It started as one single character but as these cultures split and spread apart their different experiences moulded that original story into different forms

This is similar to the European and Aryan story/belief of the sacred cow which is told in different forms among Indo-European speakers but today mostly associated with the Hindus

wetdspace:
Yeah I watched a similar documentary about the hormones or genes of Africans transformed from homosapience to humans and they were changed by —oh I forgot their name.

There could be a large amount of truth in it because have heard some stories as well about a particular town in Yoruba where some large amount of trees were turned to humans...

Some other stories where humans were made from a thing just for the purpose of mass farming.

Where do we categorize babies gotten from the gods, where do those babies come from and where are they presently?

What about those Iwins, Oro’s and egbere that exists in our stories then, where are those things now in our modern world?

If the truth could be found, it would explain a lot of things...

This is deep.
I hope people will just look into how this spiritism could affect genetic change