The Forgotten Exodus: The Into Africa Theory of Human Evolution

whitecoast

The Living Force
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Although I don’t really have much to contribute on this topic so far, I really enjoyed the Into Africa book, and all the data being assembled here by everyone is very helpful to get a better grasp of the subject in all it’s nuances, so thanks.

I thought some of the evidence the author brought up in passing of Homo erectus living on islands that couldn’t have been reached by land was mind-blowing.
 
from paleoanthropologist John Hawks:

Until now, scientists have mostly assumed that the Philippines were first inhabited by modern humans, only after 100,000 years ago. But the artifacts unearthed by Ingicco and coworkers were much older, more than 700,000 years old.
...
Who were these ancient islanders, and how did they manage these deepwater crossings so long ago?
This is where scientists may find the next hobbits – John Hawks – Medium

bonus: beautiful picture of "Callao Cave" (click image for larger image)!
 

Voyageur

The Living Force
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Jeffrey of Troy said:
from paleoanthropologist John Hawks:


Until now, scientists have mostly assumed that the Philippines were first inhabited by modern humans, only after 100,000 years ago. But the artifacts unearthed by Ingicco and coworkers were much older, more than 700,000 years old.
...
Who were these ancient islanders, and how did they manage these deepwater crossings so long ago?
This is where scientists may find the next hobbits – John Hawks – Medium

bonus: beautiful picture of "Callao Cave" (click image for larger image)!
That is a nice looking cave indeed.

Kind of a repeat here, yet when looking again at the maps, those from that Hawks link; the land masses, islands and jetties, and then factoring the significantly lower sea levels, one wonders re Hawks question, that 'managing' it may have been relatively simple. It seems perhaps that we have made it problematical because there is obviously difficulties with physical evidence, let alone fathoming the possibilities of ancient kinds even doing this.

Was reminded of this article: 13,800-year-old Haida site found 400 ft. underwater in Canada whereby the depth is stated. Going back a few pages here, the rise was said to be 150m (near 500ft). So, can we really know when adding so much additional time if it was not much lower than 150m? If that could be concidered; and how much so I've know idea (200m - 500m?), these ancient ones could have almost walked.
 

Laura

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That is a nice looking cave indeed.

Kind of a repeat here, yet when looking again at the maps, those from that Hawks link; the land masses, islands and jetties, and then factoring the significantly lower sea levels, one wonders re Hawks question, that 'managing' it may have been relatively simple. It seems perhaps that we have made it problematical because there is obviously difficulties with physical evidence, let alone fathoming the possibilities of ancient kinds even doing this.

Was reminded of this article: 13,800-year-old Haida site found 400 ft. underwater in Canada whereby the depth is stated. Going back a few pages here, the rise was said to be 150m (near 500ft). So, can we really know when adding so much additional time if it was not much lower than 150m? If that could be concidered; and how much so I've know idea (200m - 500m?), these ancient ones could have almost walked.
I think they have geological ways of determining water levels at various times.

What they are really grappling with is their assumption that human beings - in whatever form - were too dumb to do stuff because they didn't leave a whole lot of stone tools and such.

One of the interesting theories about why there are not a lot of stone tools found in the East was because they used bamboo for about everything even from a very early time. That not all tools of modern type humans were stone seems pretty obvious.
 

Voyageur

The Living Force
FOTCM Member
Laura said:
I think they have geological ways of determining water levels at various times.

What they are really grappling with is their assumption that human beings - in whatever form - were too dumb to do stuff because they didn't leave a whole lot of stone tools and such.

One of the interesting theories about why there are not a lot of stone tools found in the East was because they used bamboo for about everything even from a very early time. That not all tools of modern type humans were stone seems pretty obvious.
Yes, point taken - it's commensurate with a shelf (say 200m +/-) and the rest is darn deep.

Spot on about the bamboo etc. and our assumptions. And if indeed it's an information universe that can be accessed, then there is no reason to think it was not accessed even back in time to one extent or another. People needed to get from A to B and could figure out the means to do so.

Looked around at some of the dating systems and depths and generally they fluctuate from 120 - 150m for the time periods, which was said, and greater going back in the millions of years - here is graph - the Exxon Sea curve went pretty deep, but a long time ago:





Going back to Australia, thought this little mention of aboriginals linguistic history was interesting as it relates: Ancient Sea Rise Tale Told Accurately for 10,000 Years

[...]
To most of us, the rush of the oceans that followed the last ice age seems like a prehistoric epoch. But the historic occasion was dutifully recorded—coast to coast—by the original inhabitants of the land Down Under.

Without using written languages, Australian tribes passed memories of life before, and during, post-glacial shoreline inundations through hundreds of generations as high-fidelity oral history. Some tribes can still point to islands that no longer exist—and provide their original names.

That’s the conclusion of linguists and a geographer, who have together identified 18 Aboriginal stories—many of which were transcribed by early settlers before the tribes that told them succumbed to murderous and disease-spreading immigrants from afar—that they say accurately described geographical features that predated the last post-ice age rising of the seas.

“It’s quite gobsmacking to think that a story could be told for 10,000 years,” Nicholas Reid, a linguist at Australia’s University of New England specializing in Aboriginal Australian languages, said. “It’s almost unimaginable that people would transmit stories about things like islands that are currently underwater accurately across 400 generations.

How could such tales survive hundreds of generations without being written down?
[...]
Nunn has drafted a paper describing sea level rise history in the 18 identified Aboriginal Australian stories, which he plans to publish in a peer-reviewed journal. He’s also scouring the globe for similar examples of stories that describe ancient environmental change.
[...]
This goes on to list other areas with oral tradition past down:

Port Phillip Bay
Kangaroo Island
Tiwi Islands
Rottnest, Carnac and Garden Islands

Fitzroy Island
Spencer Gulf


This is a link to the actual paper which I can't download. Indigenous Australian stories and sea-level change | USC Research Bank - University of the Sunshine Coast
 

Laura

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Sometimes you just have to scratch your head at the obvious blindness of so-called scientists.


When did Aboriginal people first arrive in Australia?
August 7, 2018 by Alan Cooper, Alan N Williams, Nigel Spooner, The Conversation


Read more at: When did Aboriginal people first arrive in Australia?

Many Aboriginal Australians would say with conviction that they have always been here. Their ancestors and traditional learnings tell them of this history, and their precise place within it.

Our review of the scientific evidence, published today in Proceedings of the National Academy of Sciences, suggests that for all practical purposes, this is indeed the case.
Their ancestors arrived shortly after 50,000 years ago – effectively forever, given that modern human populations only moved out of Africa 50,000-55,000 years ago.
Long connection to country
Earlier genetic analysis of historic Aboriginal hair samples confirmed the incredibly long and deep relationships between individual Aboriginal groups and their particular country. The small locks of hair were collected during anthropological expeditions across Australia from the 1920s to the 1960s.
Analysis of maternal genetic lineages revealed that Aboriginal populations moved into Australia around 50,000 years ago. They rapidly swept around the west and east coasts in parallel movements—meeting around the Nullarbor just west of modern-day Adelaide.
Archaeological sites and dates (shown above) closely match the genetic estimates. This indicates a very rapid movement throughout Australia 48,000-50,000 years ago.
Out of Africa
It was only a few thousand years earlier that a small population of modern humans moved out of Africa. As they did, they met and briefly hybridised with Neandertals before rapidly spreading around the world.
They became the genetic ancestors of all surviving modern human populations outside of Africa, who are all characterised by a distinctive small subset of Neandertal DNA – around 2.5% – preserved in their genomes.
This distinctive marker is found in Aboriginal populations, indicating they are part of this original diaspora, but one that must have moved to Australia almost immediately after leaving Africa.
How to get to Australia 50,000 years ago
The movement from Africa to Australia culminated in a series of hazardous sea voyages across island southeast Asia.



Recent studies suggest the last voyage, potentially between Timor/Roti and the northern Kimberley coast, would have involved advanced planning skills, four to seven days paddling on a raft, and a total group of more than 100 to 400 people.
The possibility that earlier waves of modern human populations might have moved out of Africa before 50,000 years has also been raised.
But in our review of these events, we point out that there is no convincing fossil evidence to support this idea beyond the Middle East.
One of the most important claimed potential early sites is in northern Australia, at Madjedbebe, a rock shelter in Arnhem Land. Human presence here was recently declared at more than 65,000 years ago.
This 65,000-year date has rapidly become accepted as the age for colonisation of Australia. It has appeared widely in the media and elsewhere, in political statements and comments by the Prime Minister.
But there is good reason to question a 65,000-year date, and the extent to which this contrasts with the sudden wave of archaeological sites that sweep across Australia shortly after 50,000 years ago.
These sites include Barrow Island and Carpenters Gap in the Kimberley, Devils Lair south of Perth, Willandra Lakes in NSW, and Warratyi rockshelter in the Flinders Ranges.
This rapid archaeological manifestation at 50,000 years is a perfect match for the genetic evidence from Aboriginal maternal, paternal, and genomic lineages, and a far better fit with the extinction of Australia's megafauna around 42,000 years ago.
An age limit for human migration
One of the most interesting ways we can date the dispersal of modern humans around the globe, including Australia, is through that original interbreeding event with Neandertals as we left Africa.
About a decade ago, an ancient human leg bone was found on the banks of a Siberian river by an ivory hunter. Radiocarbon-dated at 43,000-45,000 years ago, the entire genome of this individual, named Ust'-Ishim after the site, was sequenced using the latest ancient DNA technology.
The genomic sequence revealed the bone contained the standard 2.5% Neandertal DNA signal carried by all non-Africans. But it was still present in large continuous blocks and had yet not been dispersed into fragments around the genome as we see in more recent ancestors and ourselves.
In fact, the size of the blocks showed that the 43,000-45,000-year-old Ust'-Ishim specimen could only be a maximum of 230-430 generations after that initial Neandertal liaison, dating our movement out of Africa to no more than 50,000-55,000 years ago.
50,000 years, or more than 65,000 years?
Given the evidence is so strong that the ancestors of modern human populations only started moving around the world 50,000-55,000 years ago, could the human activity at Madjedbebe really be more than 65,000 years old?
One of the major limitations of the Madjedbebe study is that the stone artefacts themselves weren't dated, just the surrounding sand layers.
As a result, over time, even the slightest downward movement of the artefacts within the unconsolidated sand layers at Madjedbebe would make them appear too old.
We identify a range of factors which are common around the site, such as termite burrowing and heavy rainfall, that could cause stone artefacts to sink.
Many archaeological signs suggest activity at Madjedbebe is actually much younger than 65,000 years, and overall, the extent to which the site is an outlier to the rest of the Australian record should raise a red flag.
Connection to country
Either way, Aboriginal Australians have effectively been on their country as long as modern human populations have been outside of Africa.
How does this help us better understand Aboriginal history? By appreciating the enormous depth of time that Aboriginal groups have been on their own particular country, and the extent to which all their history, knowledge, and ancestors form part of that country.
It is this gulf between a European history of constant migration and global dispersal, and the profoundly deep Aboriginal connection to one particular part of the world, that leads to failures to comprehend why being on country is not simply "a lifestyle choice", but a fundamental part of their identity.
Explore further: Buried tools and pigments tell a new history of humans in Australia for 65,000 years

More information: James F. O'Connell et al. When didHomo sapiensfirst reach Southeast Asia and Sahul?, Proceedings of the National Academy of Sciences (2018). DOI: 10.1073/pnas.1808385115

Journal reference: Proceedings of the National Academy of Sciences


Read more at: When did Aboriginal people first arrive in Australia?
 

Eboard10

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A study has been released about the bone fragment of a 13 years old child from the Denisova Cave in Russia who was half Neanderthal, half Denisovan suggests that these distinct species, including our own, were mixing quite regularly at the time, and proposes that they could have been absorbed into the Homo Sapiens lineage.

Neandertal mother, Denisovan father—Newly-sequenced genome sheds light on interactions between ancient hominins

Denny was an inter-species love child.

Her mother was a Neanderthal, but her father was Denisovan, a distinct species of primitive human that also roamed the Eurasian continent 50,000 years ago, scientists reported Wednesday in the journal Nature.

Nicknamed by Oxford University scientists, Denisova 11—her official name—was at least 13 when she died, for reasons unknown.

"There was earlier evidence of interbreeding between different hominin, or early human, groups," said lead author Vivian Slon, a researcher at the Max Planck Institute for Evolutionary Anthropology.

"But this is the first time that we have found a direct, first-generation offspring," she told AFP.

Denny's surprising pedigree was unlocked from a bone fragment unearthed in 2012 by Russian archeologists at the Denisova Cave in the Altai Mountains of Siberia.

Analysis of the bone's DNA left no doubt: the chromosomes were a 50-50 mix of Neanderthal and Denisovan, two distinct species of early humans that split apart between 400,000 to 500,000 years ago.

"I initially thought that they must have screwed up in the lab," said senior author and Max Planck Institute professor Svante Paabo, who identified the first Denisovan a decade ago at the same site.

Worldwide, fewer than two dozen early human genomes from before 40,000 years ago—Neanderthal, Denisovan, Homo sapiens—have been sequenced, and the chances of stumbling on a half-and-half hybrid seemed vanishingly small.

Or not.

Inter-species hanky-panky

"The very fact that we found this individual of mixed Neanderthal and Denisovan origins suggests that they interbred much more often than we thought," said Slon.

Paabo agreed: "They must have quite commonly had kids together, otherwise we wouldn't have been this lucky."

A 40,000 year-old Homo sapiens with a Neanderthal ancestor a few generations back, recently found in Romania, also bolsters this notion.

But the most compelling evidence that inter-species hanky-panky in Late Pleistocene Eurasia may not have been that rare lies in the genes of contemporary humans.

About two percent of DNA in non-Africans across the globe today originate with Neanderthals, earlier studies have shown.

Denisovan remnants are also widespread, though less evenly.

"We find traces of Denisovan DNA—less than one percent—everwhere in Asia and among native Americans," said Paabo.

"Aboriginal Australians and people in Papua New Guinea have about five percent."

Taken together, these facts support a novel answer to the hotly debated question of why Neanderthals—which had successfully spread across parts of western and central Europe—disappeared some 40,000 years ago.

Up to now, their mysterious demise has been blamed on disease, climate change, genocide at the hands of Homo sapiens, or some combination of the above.

But what if our species—arriving in waves from Africa—overwhelmed Neanderthals, and perhaps Denisovans, with affection rather than aggression?

Conquered or absorbed?

"Part of the story of these groups is that they may simply have been absorbed by modern populations," said Paabo.

"The modern humans were more numerous, and the other species might have been incorporated."

Recent research showing that Neanderthals were not, in fact, knuckle-dragging brutes makes this scenario all the more plausible.

Our genetic cousins executed sophisticated hunting strategies in groups; made fires, tools, clothing and jewellery; and buried their dead with symbolic ornaments.

They painted animal frescos on cave walls at least 64,000 years ago, well before most Homo sapiens arrived in Europe.


Far less is known about Denisovans, but they may have suffered a similar fate.

Paabo established their existence with an incomplete finger bone and two molars dated to some 80,000 years ago.

Among their [Denisovans] genetic legacy to some modern humans is a variant of the gene EPAS1 that makes it easier for the body to access oxygen by regulating the production of haemoglobin, according to a 2014 study.

Nearly 90 percent of Tibetans have this precious variant, compared with only nine percent of Han Chinese, the dominant—and predominantly lowland—ethnic group in China.


Neanderthals and Denisovans might have intermingled even more but for the fact that the former settled mostly in Europe, and the latter in central and East Asia, the researchers speculated.
 

thorbiorn

The Living Force
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After reading the articleCore problem: Human Genome Project reference is based on a single person and missing millions of DNA base pairs I wondered if there might have been a bias involved in the initial selection of the material for sequencing of the human genom.:

Over the years, we've continuously workshopped the reference genome. But recent analysis indicates that almost seventy percent of its material was gleaned from a single African-American individual, who is referred to only as RPCI-11, explains Salzburg.

That means that when scientists perform genetic analysis to identify differences between diverse populations from all over the world, most of the time, they compare those genomes to the genetic material from, mostly, one person. This leads us to often ignore material that might be too different from this reference, says Sherman. She calls them "missing pieces."
"When you line things up, there are going to be pieces that don't line up at all because they're too different to match anything from the reference genome." Sherman says. "Then you ignore all the stuff that doesn't line up as not really relevant or not really worth looking, at when maybe these are actually the pieces that are of the most interest because they're the most different from the reference genome."
So far, Sherman says, we don't really know what we're missing by ignoring DNA that's not represented in the reference genome. But who knows what we might find there if we take a look?
[...]
How Can We Fix It?

Instead of striving for a single universal reference genome, the team argues, we should have a bunch of reference genomes - perhaps one for each population of interest.

"What we're kind of advocating here with this finding, is that we really need to be building reference genomes for each population," says Sherman. "If there's this much DNA missing from the reference in this population, the model needs to change."
After fixing the holes of knowledge about the human genome, perhaps some of the current hypotheses about the origin of man will be rephrased.
 

Adaryn

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After reading the articleCore problem: Human Genome Project reference is based on a single person and missing millions of DNA base pairs I wondered if there might have been a bias involved in the initial selection of the material for sequencing of the human genom.:
Another article on the subject:

The human genome sequence, first published in 2001, has some important information missing. The latest version of it, called GRCh38, has a monstrous 3.1 gigabases of information—but that's still not enough. A letter published in Nature Genetics this week finds that the reference genome is missing a colossal 10 percent of the genetic information found in the genomes of hundreds of people with African ancestry—information that also appears in other human populations.

Get the reference
The "human genome" is in fact assembled from the genomes of just a handful of people, with the majority of GRCh38 coming from just one person. It's not a snapshot of what's in human DNA so much as a kind of template and roadmap, giving a sense of what's in there and allowing comparisons between individuals and the "reference genome."

We've known this is a limitation and have been making constant additions to the reference genome, which has improved its ability to represent the huge range of variation that's present in modern humans. But because its source is so limited, write the authors of this week's letter, so is its usefulness: "In recent years, a growing number of researchers have emphasized the importance of capturing and representing sequencing data from diverse populations."

The current situation, they write, makes it tricky to analyze people whose ancestry is very different from that of the reference genome. Although there are some methods that allow researchers to look at limited amounts of genetic diversity alongside the reference, a more comprehensive solution that's been gaining traction has been to build population-specific references—a project already underway for certain groups, including Chinese and Ashkenazi.

The genome of all humans
There is no "pan-genome"—no "collection of sequences representing all of the DNA in [a] population," write lead author Rachel Sherman and her colleagues. It's been done for bacteria, but not for humans. So they set out to create a pan-genome for Africa, using DNA from 910 people of African descent. The group includes people from the Caribbean and the US, who retain some of Africa's genetic diversity, even though they have their own distinct genetic history.

They compared the DNA from these hundreds of people to the reference genome, looking for long sections that didn't match. The basic unit of DNA is the base pair, one of the rungs on the twisted ladder that makes up the double helix. Sherman and her colleagues looked for sequences more than 1,000 base pairs long that didn't match the reference and found a lot of them: nearly 300 million base pairs, which is about 10 percent of the size of the entire reference genome.

That's not to say this information is unique to African people: about 40 percent of this data matched either the Korean or Chinese genomes. This suggests that it's important genetic material that's present across a huge range of humans, but still not captured by the reference genome assembled from just a small number of people. There's a lot going on with humans that isn't reflected by the human reference genome.

Medical consequences and cautions
Any research efforts that lean on the reference genome to study human variation will be missing out on this huge amount of data—and this is what "nearly all studies do at present," write Sherman and colleagues. "A single reference genome is not adequate for population-based studies of human genetics," they add, suggesting that a way forward is to create reference genomes for different human groups. Over time, this will lead to a pan-genome "capturing all of the DNA present in humans."

This has important consequences for medicine—"If you are a scientist looking for genome variations linked to a condition that is more prevalent in a certain population, you'd want to compare the genomes to a reference genome more representative of that population," says Rachel Sherman.

But having this information for Africans now doesn't tell us much that a scientist researching a given condition would be able to use. The study didn't explore what's being done by any of the DNA that wasn't in the reference genome and can't say anything about whether it might play a role in health conditions or any other variation.

While population-specific genomes might be a useful way forward for studying human variation, they could run into a different set of difficulties when they leave the lab and run into the real world. As demonstrated by the fact that a lot of this DNA also shows up in Koreans, population groupings between humans aren't neat lines, especially at the DNA level. They have fuzzy boundaries; individuals can have genetic traits from multiple populations; and how someone looks isn't a reliable guide to their DNA.

Complicating matters further, there are multiple populations within Africa that may have distinct genetic histories that we're just now scratching the surface of. Having a pan-African genome won't necessarily tell us a lot about what's distinctive for any individual African.

Although genetics researchers understand all of this, any use of population-specific reference genomes in fields such as medicine could come with a new swathe of problems if this messiness isn't communicated or understood well.
 
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