Human DNA tied mostly to single exodus from Africa long ago (Update)

Human DNA tied mostly to single exodus from Africa long ago (Update)
A heat map showing locations of previously unknown DNA variants. Red indicates higher number of discoveries, black fewer. Credit: Harvard Medical School

A study of hundreds of new genomes from across the globe has yielded insights into modern genetic diversity and ancient population dynamics, including compelling evidence that essentially all non-Africans today descend from a single migration out of Africa.

The multinational research effort, led by Harvard Medical School geneticists and published Sept. 21 in Nature, also suggests that no single gene can explain the significant cultural and cognitive progress in human development that occurred about 50,000 years ago.

The study represents the largest data set yet of high-quality genome sequences from understudied populations, adding nearly 6 million DNA base pairs to the "canonical" human genome sequence published in 2001.

The data identify millions of previously unknown population-specific mutations that may help scientists develop precision-targeted diagnostic tests and treatments on their quest to improve the health of the world's underserved populations.

Most genome-wide population sequencing studies to date have focused on a handful of large populations. The HMS-led study, by comparison, sequenced samples from 142 smaller populations, most of which were previously understudied.

Human DNA tied mostly to single exodus from Africa long ago
Model of the relationships among diverse humans (select ancient samples are shown in red) that fits the data. We can reject the model that Australians, New Guineans and Andamanese have substantial (more than a couple percent) ancestry from an early dispersal out of Africa. Credit: Swapan Mallick, Mark Lipson and David Reich.

"As humans, we are not just the people who live in industrialized countries, and we are not just the people who live in numerically large groups," said David Reich, professor of genetics at HMS and senior author of the study. "If we want to understand who we really are, we have to realize that some of the most interesting aspects of human variation are only present in underrepresented, small populations."

"We wanted to go out into the world and pull together as many of the ethnically, linguistically and anthropologically diverse samples as we possibly could," said Swapan Mallick, bioinformatic systems director in the Reich lab and first author of the study.

The team's analyses are already answering questions about various populations' genetic origins, but, the researchers note, these insights are only a milestone on a longer journey.

"Of course, there are thousands of ethnically distinct populations in the world, and much more work needs to be done," said Mallick.

Professor Eske Willerslev, Centre for GeoGenetics, University of Copenhagen, talking about the genetic history of the Australian Aboriginals. Credit: Natural History Museum, University of Copenhagen.

Clarifying history

Reich, Mallick and their international team of colleagues began by selecting two genomes each from 51 populations represented in a collection called the Human Genome Diversity Project. Next, they assembled samples from members of 91 other groups, including diverse Native American, South Asian, and African populations not previously included in genome-wide studies, and sent the DNA for sequencing. In all, the project analyzed the genomes of 300 people.

A key conclusion—that the vast majority of modern human ancestry in non-Africans derives from a single population that migrated out of Africa—is also supported by two other whole-genome sequencing studies appearing simultaneously in Nature. One, led by an Estonian group, focused on 379 whole genome sequences; the other, led by a Danish group, analyzed 108 Australians and New Guineans.

Together, the three studies put to rest a lingering question about whether indigenous peoples of Australia, New Guinea and the Andaman Islands descend in large part from a second group that left Africa earlier and skirted the coast of the Indian Ocean. They do not, the HMS researchers say.

"Our best estimate for the proportion of ancestry from an early-exit population is zero," said Reich, who is also an investigator of the Howard Hughes Medical Institute and associate member of the Broad Institute. "Taken together, all three studies leave wiggle room for, at most, around two percent."

The HMS-led study further revealed that the common ancestors of modern humans began to differentiate at least 200,000 years ago, long before the out-of-Africa dispersal occurred.

"It had been unclear whether the group that expanded out of Africa represented a large subset of the populations within Africa," said Mallick. "This really shows that there was a lot of substructure prior to the expansion."

Human DNA tied mostly to single exodus from Africa long ago
A graphic representation of the interaction between modern and archaic human lines, showing traces of an early out of Africa (xOoA) expansion within the genome of modern Sahul populations. Credit: Dr Mait Metspalu at the Estonian Biocentre, Tartu, Estonia

The additional discovery that genetics alone can't account for the acceleration of cultural, economic and intellectual progress in the last 50,000 years runs contrary to a popular hypothesis in the field.

"There does not seem to have been one or a few enabling mutations that suddenly appeared among our ancestors and allowed them to think in profoundly different ways," said Reich.

Instead, the researchers say, a constellation of factors, including environment, lifestyle, and possibly genes, precipitated the rapid changes that occurred.

"Geneticists often search for examples where genetics is the explanation. Here, paradoxically, genetic data are showing that there will be no clear genetic answers," Reich said.

Pagani et al, explain their results. Credit: Pagani et al. 2016

Overcoming hurdles

Mallick and colleagues overcame significant logistical hurdles posed by sharing and processing an enormous amount of data.

Often, in studies of this size, data are collected in many laboratories that use different sequencing machines and different experimental protocols. This can create so-called batch effects that make it difficult to distinguish true differences among samples. The current study minimized batch effects by sending all of the samples to a single center to be sequenced at the same time.

The team made much of the data set publicly available in 2014; multiple research groups have already used it for their studies.

In a way, the authors say, the findings reported thus far are just the tip of the iceberg.

"It's impossible for our group to analyze even a tiny fraction of what the data represents," said Mallick. "Our goal is to push the data out and let people use it to consider their own questions."


Explore further

No one is an island: The history of human genetic ancestry in Madagascar

More information: Luca Pagani et al. Genomic analyses inform on migration events during the peopling of Eurasia, Nature (2016). DOI: 10.1038/nature19792
Journal information: Nature

Citation: Human DNA tied mostly to single exodus from Africa long ago (Update) (2016, September 21) retrieved 23 July 2019 from https://phys.org/news/2016-09-human-dna-tied-exodus-africa.html
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Sep 21, 2016
Well, eight people survived the world wide flood and from them came the rest of the human population. So there was a genetic bottleneck and it did spring from a single geographic location. It just might not have been Africa, more like Ararat......
Oh, and they had agriculture from the word go. As well as metal and other kind of tool making, musical instruments and the like.

Sep 21, 2016
Well, eight people survived the world wide flood and from them came the rest of the human population.


You *are* aware this is *not* Answers in Genesis, right?

Who exactly are you trying to persuade? Can't be the readers of a *science* page, so can it be that your fear-of-death-driven belief in a bronze-age mythology is so weak, you need to drone on and on to drown the doubts in your mind (or what passes for it, anyway)? Or are you just scoring points with your unexisting vile excuse for a god, so he doesn't show his boundless love by torturing you for eternity because you failed to recruit enough mindless genuflecting slaves?

Sep 21, 2016
You *are* aware this is *not* Answers in Genesis, right?


Hell, I thought he was just joshin'. Hard to tell witty sarcasm from stupidity, I guess.

Sep 21, 2016
Hell, I thought he was just joshin'. Hard to tell witty sarcasm from stupidity, I guess.


Frankly, so did I at first. Then I seemed to remember having come across even worse bilge than this from him and realised he was for real. Reminds me of another lone warrior against the evil of evolutionism, called verkle - whenever there was an article that even mentioned the word "evolution", you could bet you favourite amber rosary he'd be there, foaming at the mouth.

It's becoming really tiring, to be fair - too many religious, tin-foil-hatted and woo-peddling trolls, not enough science sites...

Sep 21, 2016
So they start off saying everything has been cleared up. We know for sure that only group left Africa. Then at the end, they say "Oh yeah, there was another group and we really don't know anything."
Thaks a lot.

Sep 21, 2016
So they start off saying everything has been cleared up. We know for sure that only group left Africa. Then at the end, they say "Oh yeah, there was another group and we really don't know anything."
Thaks a lot.


Now go back, actually read the article, and pay attention this time. Because if that's what you got out of this article (I read it thrice) then your reading comprehension appears to be lower than the minimum required.

You're welcome.

Dug
Sep 21, 2016
Well, there goes A.G. Riddle's book thesis using the Atlantis gene concept.

Sep 22, 2016
Well, eight people survived the world wide flood and from them came the rest of the human population. So there was a genetic bottleneck and it did spring from a single geographic location. It just might not have been Africa, more like Ararat......
Unfortunately, evidence tells us there was no flood. So your myth-based hypothesis holds no water. So to speak.

There is no Mt sinai either. And your book says that moses parted a sea of reeds, not the red Sea.

Your god doesn't seem to know much about geography does he?

Sep 22, 2016
agriculture from the word go
-And that's a very curious point. Caine was a farmer and Abel a herder. This was only the 2nd Gen of people on this earth.

Dismissing the obvious question of where their wives came from, where did their domesticated plants and animals come from?

Evidence says that domestication took 1000s of years to produce these items. You claim that this 2nd Gen hit the ground with crops and herds already in place, and further they knew exactly how to take care of them.

This miracle is akin to your insistence that god created the heavens in such detail that he put each and every photon in the the proper location and sent them all on their way 6500 years ago to make appear as if his creation was billions of years old.

So not only did he wiggle his nose and poof! everything existed, he tried to trick us into thinking it happened some other way.

So what makes you think that such an incredible deceiver could be the source of all that is good and true?

Sep 22, 2016
It is a complete waste of time and effort to try and use reason with irrational followers of faith. They have long ago abandoned the ability to use independent critical thinking and have surrendered themselves to the agenda of whichever snake oil salesman they are following.

Sep 22, 2016
It is a complete waste of time and effort to try and use reason with irrational followers of faith. They have long ago abandoned the ability to use independent critical thinking and have surrendered themselves to the agenda of whichever snake oil salesman they are following.


This ^^^^^

Sep 24, 2016
Maybe he never saw the Grand Canyon before
@barfV
i've seen a water jet cut through metal, does that mean there is a flood that created the metal cut?
https://en.wikipe...t_cutter

therefore predicting a flood based upon the grand canyon is like predicting a flood based upon water being able to cut metal... and that ignores other evidence that we know and track like: riparian zones, erosion, etc
Or fossils
your own book says the flood destroyed all life (GEN 6:7) except those on the ark
(which suggest it "drowned" the fish, etc - LMFAO)

that somehow made sense to the authors as they were desert dwelling sheep/goat herders - they weren't even aware of things like fossils

.

if you're going to argue a religion, aka a "lie", you should not attempt to use evidence as that will always eventually debunk your own comments

Sep 24, 2016
@barfV cont'd
despite zero evidence of evolution
you mean you didn't read the links i left you?

tell everyone: where is the lack of evidence in any of the following studies referenced in this article?
http://www.talkor...comdesc/

i've asked you to debunk those studies with equivalent data in the past but you ignored the request

why is that?

afraid you will have to admit that there is evidence debunking your belief system?

as noted above:
if you're gonna spread a lie (religion) then you should stick to spreading your beliefs and step away from the evidence argument as it will always, always undermine your own argument

just because you believe in it doesn't mean it's true

and more to the point: your "religion" is the newcomer on the block, therefore it can't be more "real" than the older religions that pre-date it and still exist, especially as they're the foundation of your own religion ( https://en.wikipe...eligions )

Sep 25, 2016
Bart thinks that
the grand Canyon was cut by God's holy flood
-Who apparently decided it was easier and perhaps more fun to flush the entire earth and kill everything on it (including mosasaurs and plesiosaurs but not fish or whales), instead of just writing his book a few 1000 years earlier... and then offers the grand Canyon as evidence.

So happy for the opportunity to make a godder look like an idiot once again.

This lie continues to be told despite having been thoroughly debunked.
https://badscideb...-canyon/

-thereby demonstrating that believers ('the fallen') are more than willing to act as their god has taught them, and lie and cheat in his defense.

And so it is written.
http://www.evilbi...us-lied/

Ever read about the father of the chosen people?
http://probingfai...eceiver/

-By Example.

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