# Population Genetics > Paleogenetics > Paleolithic & Mesolithic >  Papuans have at least 2% of ancestry from early Out-of-Africa migration 90,000 ybp

## Maciamo

I found this news story on BBC News this morning rzlating to a new paper in Nature (Pagani et al. 2016). 


BBC News: DNA hints at earlier human exodus from Africa

_"Present-day people outside Africa were thought to descend from a group that left their homeland 60,000 years ago.
Now, analysis of nearly 500 human genomes appears to have turned up the weak signal of an earlier migration.
But the results suggest this early wave of Homo sapiens all but vanished, so it does not drastically alter prevailing theories of our origins.

Writing in the academic journal Nature, Luca Pagani, Mait Metspalu and colleagues describe hints of this pioneer group in their analysis of DNA in people from the Oceanian nation of Papua New Guinea."

..

"Yet we had known for some time that groups of modern humans made forays outside their "homeland" before 60,000 years ago.

_
_Fossilised remains found at the Qafzeh and Es Skhul caves in Israel had been dated to between 120,000 and 90,000 years ago.__Then in 2015, scientists working in Daoxian, south China, reported the discovery of modern human teeth dating to at least 80,000 years ago.__An additional piece of evidence recently came from traces of Homo sapiens DNA in a female Neanderthal from Siberia's Altai mountains. The analysis suggested that modern humans and Neanderthals had begun mixing around 100,000 years ago - presumably outside Africa."_
_...

"The first instance when we thought we were seeing something was when we used a technique called MSMC, which allows you to look at split times of populations," said co-author Dr Mait Metspalu, director of the Estonian Biocentre in Tartu, told BBC News.

His colleague and first author Dr Luca Pagani, also from the Estonian Biocentre, added: "All the other Eurasians we had were very homogenous in their split times from Africans.

"This suggests most Eurasians diverged from Africans in a single event... about 75,000 years ago, while the Papuan split was more ancient - about 90,000 years ago. So we thought there must be something going on."
It was already known that Papuans, along with other populations from Oceania and Asia, derive a few per cent of their ancestry from Denisovans, an enigmatic sister group to the Neanderthals.

The researchers tried to remove this component, but were left with a third chunk of the genome which was different from the Denisovan segment and the overwhelming majority which represents the main out of Africa migration 60,000 years ago."

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The paper mentions that no mtDNA or Y-DNA dating from that Early Out-of-Africa (OoA) migration was identified among Papuans.




> Y chromosome and mtDNA haplopgroup analysis. The presence of an extinct xOoA trace in the genome of modern Papuans may seem at odds with analyses of mtDNA and Y chromosome phylogenies, which point to a single, recent origin for all non-African lineages (mtDNA L3, which gives rise to all mtDNA lineages outside Africa has been dated at ~ 70,000 years old). However, uniparental markers inform on a small fraction of our genetic history, and a single origin for all non-African lineages does not exclude multiple waves OoA from a shared common ancestor. We show analytically (Supplementary Information 2.2.12) that, if the xOoA signature entered the genome of Papuan individuals > 40 kya, their mtDNA and Y lineages could have been lost by genetic drift even assuming an initial xOoA mixing component of up to 35%.

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## bicicleur

it all sounds quite logical to me
by 120 ka, after the ice age before the last there were 3 modern human populations in SW Asia
- Skhull, Qafzeh caves 120 ka in the Levant, who's skulls are related to the 160 ka Irhoud skulls in the Atlas Mountains
around 90 ka these were replaced by incoming Neanderthals and fractions of their DNA has been found in the Altai Neanderthal 50 ka
- Jebel Faya 128 ka near the Persian Gulf who's tools were similar to the Abdur reef tools, Red Sea coast
IMO some of these people went further east and let their teeth in Doaxian, southwest China, and fractions of their DNA in the Papuans
I guess the very first people in Australia descend also from these people
- Dhofar, South-Arabian coast, Nubyan Complex tools, one dated 106 ka but probably older exist as well
IMO this is haplogroup BT who expanded first into Arabia, later into northeast Africa, Sundaland, the Levant, Central Asia, Europe, in short the ancestor of all non-SSA present day humans

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## Angela

[QUOTE=Angela;490535]Pagani et al: Genomic analyses inform on migration events during the peopling of Eurasia
http://www.nature.com/nature/journal...ture19792.html

"Absract: High-coverage whole-genome sequence studies have so far focused on a limited number1 of geographically restricted populations (2, 3, 4, 5) or been targeted at specific diseases, such as cancer6. Nevertheless, the availability of high-resolution genomic data has led to the development of new methodologies for inferring population history (7, 8, 9) and refuelled the debate on the mutation rate in humans (10). Here we present the Estonian Biocentre Human Genome Diversity Panel (EGDP), a dataset of 483 high-coverage human genomes from 148 populations worldwide, including 379 new genomes from 125 populations, which we group into diversity and selection sets. We analyse this dataset to refine estimates of continent-wide patterns of heterozygosity, long- and short-distance gene flow, archaic admixture, and changes in effective population size through time as well as for signals of positive or balancing selection. We find a genetic signature in present-day Papuans that suggests that at least 2% of their genome originates from an early and largely extinct expansion of anatomically modern humans (AMHs) out of Africa. Together with evidence from the western Asian fossil record (11), and admixture between AMHs and Neanderthals predating the main Eurasian expansion (12), our results contribute to the mounting evidence for the presence of AMHs out of Africa earlier than 75,000 years ago."


They also have a youtube video out on it:
https://www.youtube.com/watch?v=z9LRdoMeXC4

Malaspinas et al: Nature _Nature, Published online 21 September 2016, doi:10.1038/nature18299_

""Abstract: The population history of Aboriginal Australians remains largely uncharacterized. Here we generate high-coverage genomes for 83 Aboriginal Australians (speakers of Pama–Nyungan languages) and 25 Papuans from the New Guinea Highlands. We find that Papuan and Aboriginal Australian ancestors diversified 25–40 thousand years ago (kya), suggesting pre-Holocene population structure in the ancient continent of Sahul (Australia, New Guinea and Tasmania). However, all of the studied Aboriginal Australians descend from a single founding population that differentiated ~10–32 kya. We infer a population expansion in northeast Australia during the Holocene epoch (past 10,000 years) associated with limited gene flow from this region to the rest of Australia, consistent with the spread of the Pama–Nyungan languages. We estimate that Aboriginal Australians and Papuans diverged from Eurasians 51–72 kya, following a single out-of-Africa dispersal, and subsequently admixed with archaic populations. Finally, we report evidence of selection in Aboriginal Australians potentially associated with living in the desert.""

Analyses of it, which is helpful because the article is behind a pay wall:
http://phys.org/news/2016-09-unprece...migration.html
http://www.sci-news.com/genetics/ancestry-indigenous-australians-04211.html

Mallick et al: (The Reich group), for a contrary view:

The Nature version is, as always, behind a pay wall, but the Reich group, also as always, provides a version of it on their own website.
https://genetics.med.harvard.edu/reich/Reich_Lab/Publications_files/SGDP_SNP_paper_Nature.pdf

"Here we report the Simons Genome Diversity Project data set: high quality genomes from 300 individuals from 142 diverse populations. These genomes include at least 5.8 million base pairs that are not present in the human reference genome. Our analysis reveals key features of the landscape of human genome variation, including that the rate of accumulation of mutations has accelerated by about 5% in non-Africans compared to Africans since divergence. We show that the ancestors of some pairs of present-day human populations were substantially separated by 100,000 years ago, well before the archaeologically attested onset of behavioural modernity. We also demonstrate that indigenous Australians, New Guineans and Andamanese do not derive substantial ancestry from an early dispersal of modern humans; instead, their modern human ancestry is consistent with coming from the same source as that of other nonAfricans."

A nice analysis of the paper:
http://phys.org/news/2016-09-human-dna-tied-exodus-africa.html


David Reich's comments on the discrepancy:
""In our paper, we exclude more than about 2% ancestry in Australians, Papuans, and New Guineans from an early dispersal population, and our best estimate is 0%.

"I am a bit concerned that poorly modelled features of the methods used by Pagani and colleagues may have contributed to a false-positive signal of early dispersal ancestry in them. However, an alternative possibility is that the truth is around 2%, and this might just be consistent with all three studies.""

Chris Striger:
"My take on the 4 Out of Africa and human genome diversity and evolution papers in Nature this week...
https://twitter.com/ChrisStringer65/...43767733657600

He also obviously discusses a Timmerman et al paper correlating climate change and migrations. See:
http://www.archaeology.org/news/4859...les-simulation

The paper and Stringer's article on it are both behind a pay wall.

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## Maciamo

I already posted about this paper here.

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## Angela

Since this contains info about three related papers, do you want to merge the threads?

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## holderlin

Wow Papuans have it all. They must have some super powers. 

Do they also have Neanderthal or is Denisovan the only archaic in them? 

Was is also Papuans who appeared to have another segment of unidentified archaic homonin?

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