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DD'eDeN
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https://anthropology.net/2017/10/07/vindija-33-19s-genome-shows-we-are-more-neanderthal-than-we-thought/

Last year, it was suggested Neanderthals starting breeding with archaic modern humans around 100,000 years ago. These two new papers pushes that back even further to between 130,000 to 145,000 years ago. And location of these sub-species encounters probably happened in the Middle East or the Arabian Peninsula, and before modern humans spread en masse into Europe and Asia.
When comparing Vindija 33.19 genome to the UK Biobank database, with 112,338 modern individuals, the group identified that modern populations carry between 1.8 to 2.6% of Neanderthal DNA, which is higher than the previous estimates of about 1.5 to 2.1%. Curiously, East Asians carry about 2.3 to 2.6% Neanderthal DNA, while people from western Europe and Asia, on the other hand have retained about 1.8 to 2.4% DNA. African populations have virtually none because their ancestors did not mate with Neanderthals.

Straight hair from Neanderthals

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xyambuatlaya

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the earlier estimate for Neanderthal-human was 1-4%

and Denisova 3% to 5% of the DNA of Melanesians and Aboriginal Australians

One recent article was talking about evidence of a different hominid
mixture detected in an African sample

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DD'eDeN
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https://anthropology.net/2017/10/12/on-the-evolution-of-skin-tones-in-africa/

Evolutionary geneticist Sarah Tishkoff of the University of Pennsylvania, the lead author of the new study measured the reflectance of light on the skin of 2,092 people from Ethiopia, Tanzania, and Botswana along with Nicholas Crawford. The eastern African groups, like the Mursi and Surma, had the darkest skin on objective reflectance assessments, and the lightest are the San with shades between such as the Agaw.

Concurrently, they collected blood samples of 1,570 of these people for genetic studies and sequenced more than 4 million SNPs. They found 8 sites of the human genome that are particularly associated with the level of skin pigmentation which makes up for 30% of the variation in skin tone we see. Four key areas of the genome, which emerged 900,000 years ago, have specific SNPs that correlate directly with skin color.

SLC24A5, that gene I commented on before, and that we’ve known about for over 12 years to be associated with lighter skin tones, is common in some Ethiopian populations. Variants of this gene appeared 30,000, likely from Middle Eastern groups returning to eastern Africa. Variants of two neighboring genes, HERC2 and OCA2, which are also associated with light skin, eyes, and hair phenotypes seen in Europeans ultimately arose in Africa. The SNPs we see in Europeans are ancient and common in the light-skinned San people. The team proposes that these SNPs arose in Africa over 1 million years ago and spread later to Europeans and Asians. Which is incredible and I’ll comment on later.

I think the most dramatic discovery is of MFSD12. Two SNPs which decrease expression of this gene were found in high frequencies in people with the darkest skin. They confirmed in culture cells that these mutant MFSD12 genes lead to more eumelanin. These variants arose about a 500,000 years ago, suggesting that human ancestors before that time may have had moderately dark skin, rather than the deep black hue created today by these mutations. These same two variants are found in Melanesians, Australian Aborigines, and some Indians, which implies that these groups may have inherited the variants from ancient migrants from Africa who followed a “southern route” out of East Africa, along the southern coast of India to Melanesia and Australia.

The latest findings suggest that some particularly dark skin tones evolved relatively recently from paler genetic variants, and these people migrated out of Africa. SNPs in OCA2 and HERC2 that are associated with lighter skin are ancient, over 1 million years old and come from Africa.

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xyambuatlaya

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DD'eDeN
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http://www.gshdl.uni-kiel.de/download/calendar/4_Program5_SilkRoad_Workshop20170928.pdf

Silk Road workshop & new book, Germany...Mongols, climate, earlier periods

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xyambuatlaya

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https://anthropology.net/2017/10/14/tianyuan-man-genome-reveals-the-nuances-of-asian-prehistory/

A new study in Current Biology analyzed the entire genome of the Tianyuan man who was found near Beijing, China and lived around 40,000 years ago. The Tianyuan man’s genome marks the earliest ancient DNA from East Asia, but this is not the first time we have studied Tianyuan’s genes.

The Tianyuan skeleton was unearthed near the Zhoukoudian site, about 50 km southwest of Beijing.
In 2013 paper in PNAS, the same group that published the Current Biology paper showed there is a closer relationship of Tianyuan to present-day Asians, based off his genes, than to present-day Europeans. At that time it was suggested that present-day Asian history has a deep lineage as far back as 40,000 years ago.
In the last 4 years, we have had more data showing that modern Europeans derive from more prehistoric populations which separated early from other early non-African populations soon after the migration out of Africa. This hasn’t changed our understanding of East Asian ancestry however, showing that Tianyuan’s genetic similarity to Asians remained in comparisons including ancient Europeans without mixed ancestry…
But, most interestingly it was surprising that when they compared Tianyuan to the 35,000-year-old individual from Belgium, GoyetQ116-1, who in other ways reflected an ancient European, he shared some genetic similarity to the Tianyuan individual that no other ancient Europeans shared. This suggests that the two populations represented by the Tianyuan and GoyetQ116-1 individuals derived some of their ancestry from a sub-population prior to the European-Asian separation.

--
http://www.nbcnews.com/id/27240370/ns/technology_and_science-science/t/worlds-first-dog-lived-years-ago-ate-big/#.WeI7H7pFzDd
An international team of scientists has just identified what they believe is the world's first known dog, which was a large and toothy canine that lived 31,700 years ago and subsisted on a diet of horse, musk ox and reindeer, according to a new study.
The discovery could push back the date for the earliest dog by 17,700 years, since the second oldest known dog, found in Russia, dates to 14,000 years ago.
Remains for the older prehistoric dog, which were excavated at Goyet Cave in Belgium, suggest to the researchers that the Aurignacian people of Europe from the Upper Paleolithic period first domesticated dogs. Fine jewelry and tools, often decorated with depictions of big game animals, characterize this culture.

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xyambuatlaya

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DD'eDeN
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"Most alleles associated with light and dark pigmentation in our dataset are estimated to have originated prior to the origin of modern humans ~300 ky ago (26). In contrast to the lack of variation at MC1R, which is under purifying selection in Africa (61), our results indicate that both light and dark alleles at MFSD12, DDB1, OCA2, and HERC2 have been segregating in the hominin lineage for hundreds of thousands of years (Fig. 4). Further, the ancestral allele is associated with light pigmentation in approximately half of the predicted causal SNPs; Neanderthal and Denisovan genome sequences, which diverged from modern human sequences 804 kya (62), contain the ancestral allele at all loci. These observations are consistent with the hypothesis that darker pigmentation is a derived trait that originated in the genus Homo within the past ~2 million years after human ancestors lost most of their protective body hair, though these ancestral hominins may have been moderately, rather than darkly, pigmented (63, 64)."
N. G. Crawford et al., Science 10.1126/science.aan8433 (2017).

> Crawford, N.G., Kelly, D.E., Hansen, M.E.,
> Beltrame,
> M.H., Fan, S., Bowman, S.L., Jewett, E., Ranciaro,
> A.,
> Thompson, S., Lo, Y. and Pfeifer, S.P., 2017.
> Loci
> associated with skin pigmentation identified in
> African populations. Science, p.eaan8433.

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xyambuatlaya

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DD'eDeN
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German ape

Evidence of a chimpanzee-sized ancestor of humans but a gibbon-sized ancestor of apes.

Abstract

Body mass directly affects how an animal relates to its environment
and has a wide range of biological implications. However, little is
known about the mass of the last common ancestor (LCA) of humans and
chimpanzees, hominids (great apes and humans), or hominoids (all apes
and humans), which is needed to evaluate numerous paleobiological
hypotheses at and prior to the root of our lineage. Here we use
phylogenetic comparative methods and data from primates including
humans, fossil hominins, and a wide sample of fossil primates
including Miocene apes from Africa, Europe, and Asia to test
alternative hypotheses of body mass evolution. Our results suggest,
contrary to previous suggestions, that the LCA of all hominoids lived
in an environment that favored a gibbon-like size, but a series of
selective regime shifts, possibly due to resource availability, led to
a decrease and then increase in body mass in early hominins from a
chimpanzee-sized LCA.

https://www.nature.com/articles/s41467-017-00997-4

-

Vallesian hominid-ape-gibbon of Germany, teeth found at Rhine river 9ma, preceded African great apes by 6ma.

Lutz, H., Engel, T., Lischewsky, B. & Berg, A. von (2017): A new great ape with startling
resemblances to African members of the hominin tribe, excavated from the Mid-Vallesian Dinotheriensande of
Eppelsheim. First report (Hominoidea, Miocene, MN 9, Proto-Rhine River, Germany). – Mainzer
naturwissenschaftliches Archiv 54: xx-xx, 14 figs.; Mainz.
A new great ape with startling resemblances to African members of the hominin tribe,
excavated from the Mid-Vallesian Dinotheriensande of Eppelsheim. First report
(Hominoidea, Miocene, MN 9, Proto-Rhine River, Germany).
Herbert Lutz 1
, Thomas Engel 1
, Bastian Lischewsky 1 & Axel von Berg 2
1 Naturhistorisches Museum Mainz

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xyambuatlaya

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DD'eDeN
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http://dispatchesfromturtleisland.blogspot.com/2017/10/sorghum-domestication.html

Nice article about sorghum domestication in the Sudan, Butana "Meroe island"

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xyambuatlaya

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Clyde Winters
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quote:
Originally posted by DD'eDeN:
http://dispatchesfromturtleisland.blogspot.com/2017/10/sorghum-domestication.html

Nice article about sorghum domestication in the Sudan, Butana "Meroe island"

It is interesting that we always hear about Plant domestication beginning in the Middle East--but they never present actual sites and dates for this doemstication. Yet we do have dates for early plan domestication in Africa.

Moreover, they are finally admitting thatMillet was taken to India by Africans. I had already made this point back in 2008 web page .

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C. A. Winters

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DD'eDeN
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Tony Capra of Vanderbilt University in Nashville hypothesized last week at the annual meeting of The American Society of Human Genetics that genes we have considered to variant of Neanderthals and inherited to modern humans outside of Africa are not particularly Neanderthal genes, but rather, represent ancestral humans.

[DD: African genes, or perhaps pan-tropical-rainforest-belt-genes]

In other words, we can thank Neanderthals for giving back thousands of ancient African gene variants that were lost to Eurasians as their ancestors swept out of Africa in small bands, perhaps 60,000 to 80,000 years ago.

He and his team came about this finding by identifying African variants as they scoured the genomes of more than 20,000 people in the 1000 Genomes Project and Vanderbilt's BioVU data bank of electronic health records. Curiously they found vast stretches of chromosomes inherited from Neanderthals also carried ancient alleles, or mutations, found in all the Africans such as the Yoruba, Esan, and Mende peoples. In fact, there's about 47,261 of these SNPs across the genomes of Europeans and 56,497 SNPs in Asians. In Eurasians people, these alleles are only found next to Neanderthal genes, suggesting all this DNA was acquired at the same time, when the ancestors of today's Eurasians mated with Neanderthals roughly 50,000 years ago.
h/t Kambiz Kamrani @ Anthropology.net

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xyambuatlaya

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DD'eDeN
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Rise of East African Plateau dated by whale fossil
Old bones' elevation constrains timing of uplift that influenced human
evolution
Ashley Yeager 2015

A 17-Ma whale fossil is helping scientists pinpoint when the E.African
Plateau started to rise.
Determining when the uplift happened has implications for understanding
human evolution, scientists say.
Shifts in the Earth's mantle pushed the E.African Plateau upward between
17 & 13.5 Ma.
<http://www.pnas.org/cgi/doi/10.1073/pnas.1421502112>
Their analysis was based on a Turkana ziphiid fossil, discovered at the
edge of the plateau in Kenya in 1964.
The beaked whale's skull was described in a 1975 paper, then misplaced
until 2011, when it was rediscovered in a fossil collection kept at
Harvard.


(Moroto, Uganda, where Morotopithecus ?17 Ma was found (the first
eu-hominoid?), is now at 1380 m above sea-level --mv)


A 17-My-old whale constrains onset of uplift and climate change in east
Africa
Henry Wichura cs 2015
PNAS 112

An enigmatic fossil of the deep-diving open-ocean whale family Ziphiidae,
740 km inland, at 620 m elevation in West Turkana, Kenya was
re-discovered, after it went missing for >30 yrs.
This stranded whale fossil provides the first constraint on the initiation
of E.African uplift from near sea level at 17 Ma, limiting the timing &
initial elevation of environmental change indicated by geo-dynamic &
climatic modeling, paleo-sols, isotopes, paleo-botany & the mammalian
fossil record.
At 17 Ma,
- elevation was low,
- rainfall was high,
- vegetation was forested,
- mammalian communities contained immigrants & native African spp
incl.diverse primates.
Uplift resulted in increasing aridity & open habitats that drove human
evolution.


Timing & magnitude of surface uplift are key to understanding the impact
of crustal deformation & topographic growth on atmospheric circulation,
environmental conditions & surface processes.
Uplift of the E.African Plateau is linked to mantle processes,
but paleo-altimetry data are too scarce to constrain plateau evolution &
subsequent vertical motions associated with rifting.

Here, we assess the paleo-topographic implications of a beaked whale
fossil from the Turkana region, found 740 km inland from the present-day
coastline of the Indian Ocean, at an elevation of 620 m.
The specimen is ?17 My old,
it represents the oldest derived beaked whale known, consistent with
molecular estimates of the emergence of modern strap-toothed whales
Mesoplodon.
The whale traveled from the Indian Ocean inland along an
east-ward-directed drainage system controlled by the Cretaceous Anza
Graben,
it was stranded slightly above sea-level.
Surface uplift from near sea-level coincides with paleo-climatic change
- from a humid environment
- to highly variable & much drier conditions,
this altered biotic communities, and drove evolution in E.Africa,
including that of primates.

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xyambuatlaya

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Clyde Winters
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quote:
Originally posted by DD'eDeN:
Tony Capra of Vanderbilt University in Nashville hypothesized last week at the annual meeting of The American Society of Human Genetics that genes we have considered to variant of Neanderthals and inherited to modern humans outside of Africa are not particularly Neanderthal genes, but rather, represent ancestral humans.

[DD: African genes, or perhaps pan-tropical-rainforest-belt-genes]

In other words, we can thank Neanderthals for giving back thousands of ancient African gene variants that were lost to Eurasians as their ancestors swept out of Africa in small bands, perhaps 60,000 to 80,000 years ago.

He and his team came about this finding by identifying African variants as they scoured the genomes of more than 20,000 people in the 1000 Genomes Project and Vanderbilt's BioVU data bank of electronic health records. Curiously they found vast stretches of chromosomes inherited from Neanderthals also carried ancient alleles, or mutations, found in all the Africans such as the Yoruba, Esan, and Mende peoples. In fact, there's about 47,261 of these SNPs across the genomes of Europeans and 56,497 SNPs in Asians. In Eurasians people, these alleles are only found next to Neanderthal genes, suggesting all this DNA was acquired at the same time, when the ancestors of today's Eurasians mated with Neanderthals roughly 50,000 years ago.
h/t Kambiz Kamrani @ Anthropology.net

These researchers have misinterpreted the data. If Neanderthals acquired the genes 50kya they were carried there by Africans, not Eurasians as assumed by the authors of this study.

The most interesting thing about their findings is that the Mande expanded all the way up to China, and the Yoruba lived in Anatolian for an extended period of time before they migrated back into Africa.

--------------------
C. A. Winters

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the lioness,
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quote:
Originally posted by Clyde Winters:
quote:
Originally posted by DD'eDeN:
[qb] Tony Capra of Vanderbilt University in Nashville hypothesized last week at the annual meeting of The American Society of Human Genetics that genes we have considered to variant of Neanderthals and inherited to modern humans outside of Africa are not particularly Neanderthal genes, but rather, represent ancestral humans.

[DD: African genes, or perhaps pan-tropical-rainforest-belt-genes]

In other words, we can thank Neanderthals for giving back thousands of ancient African gene variants that were lost to Eurasians as their ancestors swept out of Africa in small bands, perhaps 60,000 to 80,000 years ago.

He and his team came about this finding by identifying African variants as they scoured the genomes of more than 20,000 people in the 1000 Genomes Project and Vanderbilt's BioVU data bank of electronic health records. Curiously they found vast stretches of chromosomes inherited from Neanderthals also carried ancient alleles, or mutations, found in all the Africans such as the Yoruba, Esan, and Mende peoples. In fact, there's about 47,261 of these SNPs across the genomes of Europeans and 56,497 SNPs in Asians. In Eurasians people, these alleles are only found next to Neanderthal genes, suggesting all this DNA was acquired at the same time, when the ancestors of today's Eurasians mated with Neanderthals roughly 50,000 years ago.
h/t Kambiz Kamrani @ Anthropology.net

These researchers have misinterpreted the data. If Neanderthals acquired the genes 50kya they were carried there by Africans, not Eurasians as assumed by the authors of this study.


Modern day Africans have very little to no Neanderthal DNA but recent research suggests admixture of Afruwith other hominids in Africans

http://www.buffalo.edu/news/releases/2017/07/028.html

_____________________________


Dispersals out of Africa

Anatomically modern humans originated in Africa by about 200,000 years ago. The accepted theory is that there were two dispersals from African populations,[12][35] an early one via northern Africa which left traces in some human populations,[36] and a second one which populated the entire world.

The first dispersal took place between 130,000–115,000 years ago via northern Africa, but died out or retreated.[3][4][5][6] Chinese researchers question this extinction, claiming that modern humans were present in China already 80,000 years ago.[7]

A second dispersal took place via the so-called Southern Route, either before[37] or after[12][13] the Toba event, which happened between 69,000 and 77,000 years ago.[37] This dispersal followed the southern coastline of Asia, crossing about 250 kilometres (155 mi) of sea, and colonized Australia by around 65,000-50,000 years ago. According to this theory, Europe was populated either by a migration out of India, which was repopulated from southeast Asia after the Toba-event (pre-Toba hypothesis), or by an early offshoot which settled the Near East and Europe (post-Toba hypothesis).[12][13]

Nonetheless, in July 2017, evidence suggests that Homo sapiens may have migrated from Africa as early as 270,000 years ago, much earlier than the 70,000 years ago thought previously

.
___________________________________________

Therefore human admixture with Neanderthals could have taken place in the middle east.
Modern day Africans have very little to no Neanderthal DNA

____________________________

Proportion of admixture

The proportion was estimated to be 1.5–2.1% in Prüfer et al. (2013),[3] but it was later revised to a higher 1.8–2.6% and it was noted that East Asians carry more Neandertal DNA (2.3-2.6%) than Western Eurasians (1.8-2.4%) in Prüfer et al. (2017).[4] Lohse and Frantz (2014) infer an even higher rate of 3.4–7.3%.[5]

_______________________________


The proportions are not very high

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DD'eDeN
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The region with the strongest associations was in and around the SLC24A5 gene, one variant of which is known to play a role in light skin color in European and some southern Asian populations and is believed to have arisen more than 30,000 years ago. This variant was common in populations in Ethiopia and Tanzania that were known to have ancestry from southeast Asia and the Middle East, suggesting it was carried into Africa from those regions and, based on its frequency, may have been positively selected.

Another region, which contains the MFSD12 gene, had the second strongest association to skin pigmentation. This gene is expressed at low levels in depigmented skin in individuals with vitiligo, a condition where the skin loses pigment in some areas.

"I still rememeber the 'ah ha!' moment when we saw this gene was associated with vitiligo," said Crawford. "That's when we knew we'd found something new and exciting."

The team found that mutations in and around this gene that were associated with dark pigmentation were present at high frequencies in populations of Nilo-Saharan ancestry, who tend to have very dark skin, as well as across sub-Saharan populations, except the San, who tend to have lighter skin. They also identified these variants, as well as others associated with dark skin pigmentation, in South Asian Indian and Australo-Melanesian populations, who tend to have the darkest skin coloration outside of Africa.

"The origin of traits such as hair texture, skin color and stature, which are shared between some indigenous populations in Melanesia and Australia and some sub-Saharan Africans, has long been a mystery." Tishkoff said. "Some have argued it's because of convergent evolution, that they independently evolved these mutations, but our study finds that, at genes associated with skin color, they have the identical variants associated with dark skin as Africans.

"Our data are consistent with a proposed early migration event of modern humans out of Africa along the southern coast of Asia and into Australo-Melanesia and a secondary migration event into other regions. However, it is also possible that there was a single African source population that contained genetic variants associated with both light and dark skin and that the variants associated with dark pigmentation were maintained only in South Asians and Australo-Melanesians and lost in other Eurasians due to natural selection."
Read more at https://archaeologynewsnetwork.blogspot.com/2017/10/genes-responsible-for-diversity-of.html#7GScshZBu5ffpee7.99

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xyambuatlaya

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DD'eDeN
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A collection of 27 fragmented statues of the lioness goddess Sekhmet has been uncovered during excavation work at the King Amenhotep III funerary temple at the Kom El-Hettan area on Luxor’s west bank.
The discovery was made by an Egyptian-European archaeological mission led by archaeologist Hourig Sourouzian as part of the King Amenhotep III Temple Conservation Project

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xyambuatlaya

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