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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 lioness,
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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.

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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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DD'eDeN
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Oman was home to a civilisation almost 4,000 years old and had contacts with parts of present day Pakistan, a study has confirmed.

[Note: The Shahra of Oman raise cattle in dome huts and caves, where they burn frankinsence to fumigate.It is the only place in Arabia that has kept cattle continuously, other places became desert.]

“There are initial indications of its external relations with Sindh, in which the pottery or the storage jar, which was manufactured in the civilisation of Harappa, then in Sindh,” a statement from the university read.

It is believed that the place of manufacture of the pottery found in Dahwa is located in the central region of the Sindh valley in Pakistan, specifically the Mohenjodaro region, where archaeologists found the largest city in the world dating back to the early Bronze Age (2500-2000 BC).

Archaeologists also believe that this pottery was used to transport some products from the Indus Valley by small boats across the Indus River to the shores of the Arabian Sea. They were transported by larger boats to a port near the wilayat of Saham and then were carried on shoulders for 24 kilometers inwards through the edges of the Hajar Mountains to the Dahwa area. The strong presence of Sindh pottery in Dahwa indicates the extent of trade activity that prevailed between the Oman and Sindh during the early Bronze Age.

The nature of the materials that were imported from Sindh and transported in these jars has not yet been identified. It is known that the Oman was famous for the export of copper to Sindh, Mesopotamia and Iran during the period of Umm Al Nar (Mother of fire) culture.

Read more at https://archaeologynewsnetwork.blogspot.com/2017/12/artefacts-show-indus-valley-omani.html#kpGEBREMHF0TqmJf.99

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xyambuatlaya

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DD'eDeN
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https://www.livescience.com/61285-stone-tools-found-in-saudi-arabia.html
>
> More than 1,000 stone artifacts, some of which may be up to 1.76 million years old, have been discovered at Wadi Dabsa, in southwest Saudi Arabia near the Red Sea.
>
> The artifacts, which were found in what is now an arid landscape, date to a time when the climate was wetter; they may provide clues as to how and when different hominins left Africa, researchers said.
>
> The stone artifacts include the remains of hand axes, cleavers (a type of knife), scrapers (used to scrape the flesh off of animal hides), projectile points (that would have been attached to the ends of spears), piercers (stone tools that can cut small holes through hide or flesh) and hammer stones

-

Sheba/Saaba, Dedan, Asir/Asshur linked

Genesis 25:3 Commentaries: Jokshan became the father of Sheba ...

biblehub.com/commentaries/genesis/25-3.htm

Sheba, Dedan, and Asshurim are recurring names Genesis 10:7, Genesis 10:22, Genesis 10:28, describing other tribes of Arabs equally unknown. The three sons of Dedan may be traced in the tribe Asir of the south of Hejaz, the Beni Leits of Hejaz, and the Beni Lam of the borders of Mesopotamia.

https://www.livescience.com/61285-stone-tools-found-in-saudi-arabia.html

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xyambuatlaya

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Papuans in Brazil 11.5ka

http://www.pnas.org/content/102/51/18309.full new article

11.5ka Luzia et. al. at Lagoa Santa Karst rockshelters, unique morphology.

Near region of the "Melanesian" genetic trace:
(from 2015) http://www.sciencemag.org/news/2015/07/mysterious-link-emerges-between-native-americans-and-people-half-globe-away
-

Luzia et al ancestors were from a SEAsian-Papuan group that used bark-canoes (from Sago palm processing) riding the north Pacific Gyre of the warm-water Kuroshio current going up the Pacific coast when Beringia blocked today's cold Arctic current, northeastward-eastward (south of Beringia) then southward to California & Honduras to the equator where they met the northflowing Antarctic current and landed. AmerIndians arrived later from Mexico, their journey had begun earlier in Siberia. DD

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Ballito Beach boy

Being able to extract DNA and then sequence the full genomes of ancient human remains from tropical coasts is often considered precarious because of the warm, humid climate. Yet, we have now demonstrated the successful sequencing of full genomes (i.e. gaining the information of all chromosomes – including autosomes, X-chromosomes, Y-chromosomes and mitochondrial DNA) obtained from Stone Age human remains found along the tropical east coast of southern Africa.1 With a minimalist sampling strategy, causing the least amount of morphological damage, we sequenced genome-wide data from three sets of approximately 2000-year-old human remains found 60 years ago on the Ballito and Doonside beaches of KwaZulu-Natal, South Africa. One set of remains – those of a young boy (Figure 1) – yielded a remarkably complete genome, where every position was covered by sequenced DNA (on average) 13 times

Ancient human DNA: How sequencing the genome
of a boy from Ballito Bay changed human history


Marlize Lombard1
Mattias Jakobsson1,2,3
Carina Schlebusch1,2
AFFILIATIONS:
1Centre for Anthropological
Research & Department of
Anthropology and Development
Studies, University of
Johannesburg, Johannesburg,
South Africa
2Department of Organismal
Biology, Evolutionary Biology
Centre, Uppsala University,
Uppsala, Sweden
3SciLife Lab, Uppsala, Sweden
CORRESPONDENCE TO:
Marlize Lombard
EMAIL:
mlombard@uj.ac.za
KEYWORDS:
human genome; hunter–
gatherer; Homo sapiens;
population split-time estimations
HOW TO CITE:
Lombard M, Jakobsson M,
Schlebusch C. Ancient human
DNA: How sequencing the
genome of a boy from Ballito
Bay changed human history.
S Afr J Sci. 2018;114(1/2), Art.
#a0253, 3 pages. http://dx.doi.
org/10.17159/sajs.2018/a0253

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xyambuatlaya

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Importance of UV: EDAR evolution

Photograph of human upper incisors with significant "shoveling," anatomical variation influenced by the EDAR V370A allele alongside an increase in mammary duct branching [Credit: Christy G. Turner, II, courtesy G. Richard Scott]The genetic mutation, which probably arose 20,000 years ago, increases the branching density of mammary ducts in the breasts, potentially providing more fat and vitamin D to infants living in the far north where the scarcity of ultraviolet radiation makes it difficult to produce vitamin D in the skin.If the spread of this genetic mutation is, in fact, due to selection for increased mammary ductal branching, the adaptation would be the first evidence of selection on the human maternal-infant bond."This highlights the importance of the mother-infant relationship and how essential it has been for human survival," said Leslea Hlusko, an associate professor of integrative biology at the University of California, Berkeley.As for the teeth, it just so happens that the gene controlling mammary duct growth also affects the shape of human incisors. Consequently, as the genetic mutation was selected for in an ancestral population living in the far north during the last Ice Age, shovel-shaped incisors became more frequent too. Shoveled incisors are common among Native Americans and northeastern Asian populations but rare in everyone else.Hlusko and her colleagues outline the many threads of evidence supporting the idea in an article published this week in the journal Proceedings of the National Academy of Sciences.The finding could also have implications for understanding the origins of dense breast tissue and its role in breast cancer.For the study, Hlusko and her colleagues assessed the occurrence of shovel-shaped incisors in archeological populations in order to estimate the time and place of evolutionary selection for the trait. They found that nearly 100 percent of Native Americans prior to European colonization had shoveled incisors, as do approximately 40 percent of East Asians today.The team then used the genetic effects that are shared with dental variation as a way to discern the evolutionary history of mammary glands because of their common developmental pathway."People have long thought that this shoveling pattern is so strong that there must have been evolutionary selection favoring the trait, but why would there be such strong selection on the shape of your incisors?" Hlusko said. "When you have shared genetic effects across the body, selection for one trait will result in everything else going along for the ride."The vitamin D connectionGetting enough vitamin D, which is essential for a robust immune system and proper fat regulation as well as for calcium absorption, is a big problem in northern latitudes because the sun is low on the horizon all year long and, above the Arctic Circle, doesn't shine at all for part of the year. While humans at lower latitudes can get nearly all the vitamin D they need through exposure of the skin to ultraviolet light, the scarce UV at high latitudes forced northern peoples like the Siberians and Inuit to get their vitamin D from animal fat, hunting large herbivores and sea mammals.But babies must get their vitamin D from mother's milk, and Hlusko posits that the increased mammary duct branching may have been a way of delivering more vitamin D and the fat that goes with it.Geography of Beringia and levels of UV radiation. (A) Map of Beringia today. Cross-hatching indicates the region in which levels of UVMED (defined as the amount of UV radiation that will produce minimal erythema) that reach the Earth's surface are too low to promote cutaneous synthesis of vitamin D in humans on a year-by-year basis, requiring dietary supplementation. The black and white region marks the Arctic Circle, which has even less UV-B exposure, as would be expected from the increased latitude. The areas below the Arctic Circle in white and light blue are shallow seas as discerned from modern bathymetry, indicating land that would have been exposed during the LGM. (B) Map of Beringia during the Last Glacial Maximum showing the exposure of land at 117 meters below current sea level and the reconstructed terrestrial environments. The shrub tundra is the only area biologically productive enough to support a human population of the size estimated by molecular data. This population was genetically isolated for 2,500-9,000 years because of the ice to the east and extensive mesic tundra to the west [Credit: Leslea Hlusko, UC Berkeley]Hlusko, who specializes in the evolution of teeth among animals, in particular primates and early humans, discovered these connections after being asked to participate in a scientific session on the dispersal of modern humans throughout the Americas at the February 2017 American Association for the Advancement of Science meeting. In preparing her talk on what teeth can tell us about the peopling of the New World, she pulled together the genetics of dental variation with the archaeological evidence to re-frame our understanding of selection on incisor shape.Incisors are called "shovel-shaped" when the tongue-side of the incisors -- the cutting teeth in the front of the mouth, four on top, four on the bottom -- have ridges along the sides and biting edge. It is distinctive of Native Americans and populations in East Asia -- Korea, Japan and northern China -- with an increasing incidence as you travel farther north. Unpersuaded by a previously proposed idea that shoveled incisors were selected for use softening animal hides, she looked at explanations unrelated to teeth.The genetic mutation responsible for shoveling -- which occurs in at least one of the two copies, or alleles, of a gene called EDAR, which codes for a protein called the ectodysplasin A receptor -- is also involved in determining the density of sweat glands in the skin, the thickness of hair shafts and ductal branching in mammary glands. Previous genetic analysis of living humans concluded that the mutation arose in northern China due to selection for more sweat glands or sebaceous glands during the last ice age."Neither of those is a satisfying explanation," Hlusko said. "There are some really hot parts in the world, and if sweating was so sensitive to selective pressures, I can think of some places where we would have more likely seen selection on that genetic variation instead of in northern China during the Last Glacial Maximum."The Beringian standstillClues came from a 2007 paper and later a 2015 study by Hlusko's coauthor Dennis O'Rourke, in which scientists deduced from the DNA of Native Americans that they split off from other Asian groups more than 25,000 years ago, even though they arrived in North American only 15,000 years ago. Their conclusion was that Native American ancestors settled for some 10,000 years in an area between Asia and North America before finally moving into the New World. This so-called Beringian standstill coincided with the height of the Last Glacial Maximum between 18,000 and 28,000 years ago.According to the Beringian standstill hypothesis, as the climate became drier and cooler as the Last Glacial Maximum began, people who had been living in Siberia moved into Beringia. Gigantic ice sheets to the east prohibited migration into North America. They couldn't migrate southwest because of a large expanse of a treeless and inhospitable tundra. The area where they found refuge was a biologically productive region thanks to the altered ocean currents associated with the last ice age, a landmass increased in size by to the lower sea levels. Genetic studies of animals and plants from the region suggest there was an isolated refugium in Beringia during that time, where species with locally adaptive traits arose. Such isolation is ripe for selection on genetic variants that make it easier for plants, animals and humans to survive."If you take these data from the teeth to interpret the evolutionary history of this EDAR allele, you frame-shift the selective episode to the Beringian standstill population, and that gives you the environmental context," Hlusko said. "At that high latitude, these people would have been vitamin D deficient. We know they had a diet that was attempting to compensate for it from the archaeological record, and because there is evidence of selection in this population for specific alleles of the genes that influence fatty acid synthesis. But even more specifically, these genes modulate the fatty acid composition of breast milk. It looks like this mutation of the EDAR gene was also selected for in that ancestral population, and EDAR's effects on mammary glands is the most likely target of the selection."The EDAR gene influences the development of many structures derived from the ectoderm in the fetus, including tooth shape, sweat glands, sebaceous glands, mammary glands and hair. As a consequence, selection on one trait leads to coordinated evolution of the others. The late evolutionary biologist and author Steven Jay Gould referred to such byproducts of evolution as spandrels."This Beringian population is one example of what has happened thousands of times, over millions of years: Human populations form, exist for a little while and then disperse to form new populations, mixing with other groups of people, all of them leaving traces on modern human variation today," Hlusko said. "An important take-home message is that human variation today reflects this dynamic process of ephemeral populations, rather than the traditional concept of geographic races with distinct differences between them."Author: Robert Sanders | Source: University of California - Berkeley [April 23, 2018] Labels Anthropology, East Asia, Genetics, Indigenous Cultures, North America
TANN

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xyambuatlaya

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> Who & how? H habilis in coracles(My guess)?
> H erectus on rafts?
> Endurance runners underwater marathon?
> H Flores swimming?

http://johnhawks.net/weblog/archaeology/lower/philippines/luzon-biogeography-heaney-2018.html

John Hawks apparently agrees with me re. H habilis:

"More relevant today is that we now know that hominins occupied Flores, Sulawesi, and now Luzon, all prior to 100,000 years ago. Flores and Luzon were peopled during the early Middle Pleistocene.
What’s more, the Flores hominins may represent a hominin group that ** diverged earlier than the last common ancestor of Homo erectus ** and archaic and modern humans. **This is not a question of Homo erectus dispersing to islands**, it may be a question of a branch of hominins that–except for H. floresiensis–is presently unknown.

John PLEASE CALL THEM ** H habilis **, THE rainforest hominin, with inverted ape bowl nest domi.ciles which they inverted to make waterproof coracles to cross and follow rivers and get to nearby islands, occasionally stranding on small isles to become isolates like H floresensis hobbits.

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xyambuatlaya

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Unique video recording of a slave-ship survivor

Zora Neale Hurston and Kossula

At Language Log website

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https://phys.org/news/2015-12-engraved-schist-slab-depict-paleolithic.html#nRlv

13ka Spain engraved domi.cile on schist stone, note : no doorways, clear coiled exterior (like Mbuti Pygmy), tilted for entry/exit.

Basque hut: etxe, shield: magal
Hebrew hut: bet(h), shield: magen

Both from xyambuatlaya

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xyambuatlaya

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Sapiens.org

(Papua cultivation-processing of sago & taro flour into flatbread pancakes @44ka-24ka, followed by Jordan@14ka & Catalhoyuk@9ka bread crumbs of tubers & grains)
-

Our results, published today in the Proceedings of the National Academy of Sciences, also allowed us to reconstruct the ingredients that went into this hunter-gatherer bread. The bread makers used flour ground from wild barley, einkorn, and oat. But we also found an unexpected type of plant: tubers. Club-rush tubers, an aquatic plant of the family of papyrus (Cyperaceae), was frequently present in the archaeobotanical assemblage from Shubayqa 1. These tubers were ground into flour, mixed with cereal flour, and likely baked on a hot stone to produce a flatbread product. The hunter-gatherer bread from Jordan was a multigrain and tuber bread—not necessarily what you might expect purely in terms of maximizing calories for the labor involved. (The plant remains in the fireplace also contained a surprisingly wide variety: from tubers to grasses, seeds, and fruit.)

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xyambuatlaya

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Sweet Potato

[www.cell.com]

Behind a pay wall but here is the summary

key points:

•The sweet potato had a single origin (monophyletic) by autopolyploidy*
•Ipomoea trifida is most probably the progenitor of the sweet potato
•Ipomoea trifida had a dual role in the origin of the sweet potato
•The sweet potato arrived in Polynesia by long-distance dispersal in pre-human times

*an individual or strain whose chromosome complement consists of more than two complete copies of the genome of a single ancestral species


""he sweet potato is one of the world’s most widely consumed crops, yet its evolutionary history is poorly understood. In this paper, we present a comprehensive phylogenetic study of all species closely related to the sweet potato and address several questions pertaining to the sweet potato that remained unanswered. Our research combined genome skimming and target DNA capture to sequence whole chloroplasts and 605 single-copy nuclear regions from 199 specimens representing the sweet potato and all of its crop wild relatives (CWRs). We present strongly supported nuclear and chloroplast phylogenies demonstrating that the sweet potato had an autopolyploid origin and that Ipomoea trifida is its closest relative, confirming that no other extant species were involved in its origin. Phylogenetic analysis of nuclear and chloroplast genomes shows conflicting topologies regarding the monophyly of the sweet potato. The process of chloroplast capture explains these conflicting patterns, showing that I. trifida had a dual role in the origin of the sweet potato, first as its progenitor and second as the species with which the sweet potato introgressed so one of its lineages could capture an I. trifida chloroplast. In addition, we provide evidence that the sweet potato was present in Polynesia in pre-human times. This, together with several other examples of long-distance dispersal in Ipomoea, negates the need to invoke ancient human-mediated transport as an explanation for its presence in Polynesia. These results have important implications for understanding the origin and evolution of a major global food crop and question the existence of pre-Columbian contacts between Polynesia and the American continent.""

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https://www.andywhiteanthropology.com/blog/nations-4th-largest-metropolitan-school-district-teaching-kids-that-olmecs-were-africans

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Oldest known fishing net Korea 29,000 yrs old

Researchers also found fossilized bones belonging to fish and other animals, as well as stone tools and flakes, inside the Maedun cave, he said.

Prior to the South Korean find, the oldest fishing implements were believed to be fishing hooks, made from the shells of sea snails, that were found on a southern Japanese island and said to date back some 23,000 years

Read more at https://archaeologynewsnetwork.blogspot.com/2018/08/worlds-oldest-fishing-net-sinkers-found.html#Ar0eJEr43SSuWbxm.99
---
Pygmies were in Taiwan & Jomon Japan, so likely Korea, by then with dogs(?) and maybe bark canoes, possibly processing cycad sago(?).

Mbuti link hunting nets making an internet to form an arc, the women drive prey into it while men spear the fauna. Did Pygmies add stone sinkers to get schools of small fish in the shallows? Congo Pygmies live along crystalline streams, give birth in them to avoid inciting army ants, discarding the placenta (unlike other terrestrial & arboreal fauna but like aquatic animals), but though they fish by hand, and Wade water with nets on their shoulders, I haven't read of their use to net fish. Some Pygmies use harpoons similar to the Katanda, Uganda harpoon, which may or not be ancient.

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xyambuatlaya

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-Just Call Me Jari-
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Earliest version of our alphabet possibly discovered
Read more at https://archaeologynewsnetwork.blogspot.com/2018/05/earliest-version-of-our-alphabet.html#R4qtwlj6GTj4dd6Q.99


https://archaeologynewsnetwork.blogspot.com/2018/05/earliest-version-of-our-alphabet.html#GQjcJQqUwS4q5Bsk.97

Posts: 8805 | From: The fear of his majesty had entered their hearts, they were powerless | Registered: Nov 2007  |  IP: Logged | Report this post to a Moderator
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[QUOTE]Originally posted by -Just Call Me Jari-:
[QB] Earliest version of our alphabet possibly discovered
Read more at https://archaeologynewsnetwork.blogspot.com/2018/05/earliest-version-of-our-alphabet.html#R4qtwlj6GTj4dd6Q.99

Thanks, already saw that one, cool. I think the Phoenicians got their alphabet from constellations(Brian Pellar's Astro-Alphabet Zodiac).

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xyambuatlaya

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Well, I've found a major Paleo-etymological link:

Molimo@Bambuti: communal feast of shared offerings (antelope, fruit, cigarettes) gotten by a few young men of the band, who set a snare or net in front of each hut to "capture" the ritual donations.

The significance: molimo@Mbuti = molitva@Serbian: male lamb/ram ritually offered/snared by young men for community feast = matla@Aztec: net = malamba(?)@Philippino: net = lamb@English: young male sheep, usually killed for food and vellum/lambskin/parchment, while females were kept for reproduction & milk/cheese.

Probably related to 'Mary had a little lamb (Jesus)'. Too complex to explain now, but more coming.

See this:
http://oldeuropeanculture.blogspot.com/2018/07/aries-must-die.html

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Artif. Intel. analysis indicates human & great ape common ancestor had gorilla-like teeth.


https://www.news.com.au/technology/science/evolution/human-evolution-artificial-intelligence-offers-new-clues-to-where-or-what-we-came-from/news-story/d2939cd1aff290e97f77c6b3ddc46 016

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http://linearpopulationmodel.blogspot.com/2018/08/australian-aboriginal-bamboo-uses-and.html

Very interesting, history supports my idea of tree bark dugout canoes preceding log dugouts.

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Asian domesticated eggplant closest kin live in lowland African savanna

Eggplant's history has been obscure

The eggplant (Solanum melongena) is a species that is a member of the giant genus Solanum (around 1,400 species) within the nightshade family (Solanaceae). Solanum also accounts for two other globally important food crops, the tomato and the potato. But in contrast to these New World crops, the eggplant hails from Asia. Historical documents and genetic data have shown that the eggplant was first domesticated somewhere in the region of China and India. It is only recently, however, that taxonomists have resolved the status of the wild species that are related to the cultivated eggplant - surprisingly many of them are found in the savannahs of Africa

Read more at https://archaeologynewsnetwork.blogspot.com/2018/08/how-eggplants-became-asian-genomes-and.html#jKpWgf32ECtjbefc.99

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Dreadlocks (long) in Moluccas, Indonesia 19thC

Feather headdress on female and male Alifuru

http://s1.zetaboards.com/anthroscape/topic/8339641/1/
-
Somalia trade with China

http://anthromadness.blogspot.com/2018/09/800-ce-po-pa-li-is-not-somalia-but-1100.html?m=1
-
Sabah, Malaysia
Stone of Music: Batu Gong https://www.youtube.com/watch?v=UElHbwltLvc
Sompoton reed musical instrument http://linearpopulationmodel.blogspot.com/2015/10/sompoton-sabah-northern-borneo.html

Indian head nod at Language Log
http://languagelog.ldc.upenn.edu/nll/?p=39877

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xyambuatlaya

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,

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EDAR Gene improved infant survival of Beringians, vit. D, shovel incisor, sweat glands

https://leakeyfoundation.org/mothers-milk-holds-key/

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xyambuatlaya

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http://dispatchesfromturtleisland.blogspot.com/2018/09/vitamin-d-strikes-again-to-explain-edar.html

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Jack at AAT

Interesting fact, in 2017 they determined the Congo has been flowing uninterrupted for 17 million years, likely an impenetrable barrier.

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xyambuatlaya

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Urban forest improves math scores

https://m.phys.org/news/2018-09-schoolyard-tree-math-high-poverty-urban.html

School trees predict math success
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Bopi@Mbuti: rainforest playground/classroom

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xyambuatlaya

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Kom Ombo temple, mini-sphynx, waterlogged
https://www.nytimes.com/2018/09/25/world/middleeast/egypt-kom-ombo-temple.html

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xyambuatlaya

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Orang Jakun (Indigeonous proto-malay people) made bark canoes on Endau river, Malaysia in 1905 (photograph).

Here is a PDF document on bark canoes of Australia & SE Asia:

[English version - no photos; French version has photos]

file:///C:/Users/mbpub/Downloads/BarkCanoesAustraliaSEAsia_En.pdf

Bark-canoes of Australia and south-east Asia
(English text without illustrations)
Béat Arnold
Le tour du monde en 80 pirogues
Part Two
ARNOLD Béat, 2015. Bark-canoes of Australia and south-east Asia (English text without illustrations).
Le Locle, Editions G d’Encre (Le tour du monde en 80 pirogues, Part Two, PDF).
Translated by Jane Davis
Note: the English translation of the text is without figures (for the latter, see the original version in
French). It can be downloaded free of charge from:
www.editions-gdencre.ch/beat-arnold/103-canoe-ecorce-australie-978240501465.html

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> Temiar people of Malaysia Mountains craft rafts from giant bamboo on Nenggiri River. They call giant bamboo awen puak; rattan strips teg lok (once finished tali lok)
>
> http://linearpopulationmodel.blogspot.com/2018/10/the-manufacture-and-terminology-of.html
>
> The Manufacture and Terminology of Temiar Bamboo Rafts
>
> G. W. H. Davison
> Journal of the Malaysian Branch of the Royal Asiatic Society
> Vol. 62, No. 1 (256) (1989), pp. 97-104
> (Link)
>
> "A raft was constructed from 32 culms of the giant bamboo Gigantochloa scortechinii . . ."
>
> Related post on this blog:
>
> Towards a complete generic-level plastid phylogeny of the paleotropical woody bamboos (Poaceae: Bambusoideae)

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xyambuatlaya

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Sago palm peel & pound & sieve pith for starch flour for flat bread/pita/pan ~24ka and remaining rind/bark made with adze into bark canoe/piroge in the shape of pisang@Malay: banana or pizzle/penis/petla/post/pike. Removal of pith leaves a pit/hole/hull and a pitch/mound of flour to rinse and make pancakes.

"Pithxagro" cf !hxaro@San: bead

Very interesting match-ups.

What did Natufians 14ka call their canoes & their flat bread?

Punt? Pi(n)ta? (P)harina?
Isn't Farina an Afro-Asiatic term for flour?

Harigolu@Indic: coracle

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xyambuatlaya

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Ecological Contingency Accounts for Earliest Seagoing in the Western Pacific Ocean
Atholl Anderson
The Journal of Island and Coastal Archaeology
0:1-11, 2017
(Link)

Abstract

Seagoing at 1 mya to Flores, and sea gaps of >50 km crossed by 47 kya to Sahul, are evidence of earlier maritime migration in the western Pacific than anywhere else. Current opinion attributes the latter to the influence of anatomically modern human cultural complexity on seagoing technology and practice, together with the impetus of serial resource depression. It is argued here that seagoing was unusually advantaged in the western Pacific by a fortuitous conjunction of the warmest seas with a ready availability of large-diameter bamboo that occurred as natural rafts, and which could also be constructed into rafts large enough to transport viable colonizing groups from island to island across Wallacea to Sahul. The geography of Wallacea allowed migration solely by drifting, and exploratory landscape learning might have produced landfalls on Sahul sooner than is implied by subsistence forcing of mobility. Seagoing by drifting raft was much harder from Sahul to the east because of the virtual absence of large-diameter bamboo and longer distance to fewer or small islands; colonization occurred much later.

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xyambuatlaya

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Somalian albino cave fish lost DNA to fight UV light via visible light, unlike all other plants & animals

Clues from a Somalian cavefish about modern mammals' dark past

Posted: 11 Oct 2018 03:30 AM PDT

After millions of years living in constant darkness, a species of blind cavefish found only in Somalia has lost an ancient system of DNA repair. That DNA repair system, found in organisms including bacteria, fungi, plants, and most other animals, harnesses energy from visible light to repair DNA damage induced by ultraviolet (UV) light. A Somalian blind cavefish that, after evolving for millions of years in darkness, has lost the...

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xyambuatlaya

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Placental mammals: subterranean origins?

Modulation of DNA Repair Systems in Blind Cavefish during Evolution in
Constant Darkness
Haiyu Zhao, Giuseppe Di Mauro, Sebastian Lungu-Mitea, Daniela Vallone,
Cristiano Bertolucci & Nicholas Foulkes 2018
Curr.Biol. doi https://doi.org/10.1016/j.cub.2018.08.039

€During evolution, the cavefish P.andruzzii has lost photo-reactivation
DNA repair.
€Only P.andruzzii & placental mammals are known to lack photo-reactivation.
€The D-box enhancer coordinates DNA repair in response to ROS, UV &
visible light.
€Loss of D-box function in P.andruzzii underlies the lack of
photo.reactivation.

How does the environment shape the function & evolution of DNA repair
systems?
In a comparative study using zebrafish & the Somalian blind cavefish
Phreatichthys andruzzii, we reveal:
- during evolution for millions of years in continuous darkness,
photo-reactivation DNA repair function has been lost in P.andruzzii,
- this loss results in part from loss-of-function mutations in pivotal
DNA-repair genes:
C-terminal truncations in P.andruzzii DASH & 6-4 photolyase render these
proteins predominantly cytoplasmic, with consequent loss in their
functionality,
- a general absence of light-, UV- & ROS-induced expression of P.andruzzii
DNA-repair genes.
This results from a loss of function of the D-box enhancer element, which
coordinates & enhances DNA-repair in response to sunlight.
Apart from Placentalia, P.andruzzii iq the only species described that
lacks the highly evolutionary conserved photo-reactivation function.
In the DNA repair systems of P.andruzzii, we may be witnessing the first
stages in a process that previously occurred in the ancestors of placental
mammals during the Mesozoic era.

_____


http://blogs.discovermagazine.com/deadthings/2018/10/11/cavefish-mammal-evo
lution/#.W8f-pqZLiUl
Dead Things
Gemma Tarlach 11.10.18
Clues to the earliest days of mammal evolution may lie in the genome of
the Somalian blind cavefish, Phreatichthys andruzzii.

If you're trying to understand the earliest days of mammal evolution, the
genome of a blind cave-fish might not strike you as the most obvious place
to hunt for clues.
A study out today, however, suggests that's exactly where you can glimpse
our distant ‹ and very dark ‹ past.
Animals that live exclusively in lightless caves often share a suite of
traits (troglomorphisms):
- loss of pigmentation,
- loss of vision & of the eyes entirely.
The genomes of cave-dwellers have other (not always obvious) mutations &
changes in genetic expression (genes remain unchanged, but are turned on
or off), showing how the animal adapted to its environment over time.
Researchers discovered:
the Somalian blind cavefish shares a particular genetic quirk with nearly
all mammals that led to the loss of a light-dependent DNA repair system.
This particular DNA repair system is "highly conserved":
once it evolved, very early in the history of life, it was a trait that
was retained by virtually every living thing, from plants to animals to
even bacteria.
But not in the Somalian blind cavefish or placental mammals (every mammal
aside from 5 monotreme spp (e.g. platypus) & a couple 100 marsupials:
kangaroos, koalas, wombats, Tasmanian devils etc.).
Unlike placentals, marsupials retained a crucial DNA repair kit known as
photo-reactivation.

Lights Out

If you're a living thing on Earth exposed to sunlight (whether microbe or
megafauna), you get hit with UV radiation, which can damage your DNA:
sunlight is the most common & significant factor that leads to mutations &
other errors in the genetic code.
To promote DNA stability, organisms have DNA repair systems.
The most common DNA repair kit is "photo-reactivation", which depends on
light, and activates photolyases, that then go to town patching up an
organism's genetic blueprint.
Photoreactivation is an awesome thing ‹ and it is completely absent in
placentals & 1 little cavefish.
Placentals evolved a different DNA repair mechanism, not as efficient as
photo-reactivation, but +- gets the job done.
It's long been a puzzle in the study of mammal evolution over why & how
this large diverse group of animals lost photoreactivation, so crucial a
trait for most of the rest of life on Earth.
Enter the "nocturnal bottleneck" concept.
It was originally proposed decades ago, before genome decoding was a
thing, to explain physical & behavioral traits common to mammals, e.g.
certain thermo-regulation methods & acute hearing.
These traits could be explained, went the theory, if the earliest mammals
were generally nocturnal (most mammals today still are).
And when you look at the ebb & flow of dominant animals over millions of
years, it makes sense.
There is some disagreement over where to draw the line between true
mammals & ancestors that were on the evolutionary course to become true
mammals,
but mammals go back >160 Ma, possibly >200 Ma.
Consider what else was 160-200 Ma: dinosaurs.
Not just harmless herbivores, but a lot of swift & bitey predators.
The fossil record suggests that the earliest/nearly-mammals were small
shrew-like creatures.
Burrowing into the ground (another typical mammalian trait) & limiting
activity to night-time would have afforded some protection from hungry
dinosaurs.
Once the dinosaurs (except birds) bit the dust at the end-Cretaceous mass
extinction 65 Ma, mammals were able to diversify & evolve to occupy all
those emptied ecological niches, incl. daytime activity.
Bereft of photo-reactivation for millions & millions of years, these later
mammals evolved a different, less-efficient way to repair DNA damage.
It's not yet known exactly when placentals developed their unique DNA
repair kit.

Going To Ground

What if, however, the earliest placental mammals weren't just nocturnal?
What if they went a step further and, instead of venturing out of their
burrows only at night, didn't venture out at all?
What if they stayed safe by staying subterranean?
Let's hop back to P.andruzzii for a moment.
Unlike many other cavefish, which occasionally may be exposed to sunlight
or which have been shut off from it for merely 1000s of years, researchers
believe the Somalian blind cave-fish has lived in the absence of sunlight
for millions of years ‹ long enough, the authors say, to lose the ability
to use sunlight to repair DNA damaged by sunlight:
did P.andruzzii share a loss of photo-reactivation with placentals,
because it shares the same lightless lifestyle as the animals at the very
dawn of mammal evolution.
It's not a conclusive finding: e.g. there's no evidence that the earliest
placentals had the troglomorphisms you'd expect to find in an animal
living without light.
It's a tantalizing clue, however, that suggests maybe our very distant
forebears went through not just a nocturnal bottleneck, but a subterranean
one.
<https://www.cell.com/current-biology/fulltext/S0960-9822

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xyambuatlaya

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PPygmies in Laos

http://linearpopulationmodel.blogspot.com/2018/10/additional-evidence-for-early-modern.html?m=1

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xyambuatlaya

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My research discovery, reported at Sci.Lang Google groups:

> > > > > Gope@Papuan: shield, later decorative boards on canoes

Got it!

Gope@Papua: shield = gufa@Arb: coracle

Gufa@Arb(Tigris-Euph) = teba@Hbr: ark = topa@Hindi/kophar-c.huppa-kippa@Hbr/kupharigolu=co'racle/kufa/"gopherwood"/gope/kuphos@Grk: cup/kom@Du

Paleo-etymology is super all around the globe!¡!¡!

> > > > >
> > > > > Chimali@Azt: roundshield = sipar@Persian: roundshield
> > > > > Magal@Basque = pacal@Maya = magen/maga'an@Hbr: roundshield =
> > > > > Mongolu@Mbuti: dome moon hut \H.Arigolu@Indic: bowl sun boat ~ Argo@Grk: ark, kuphos@Grk: cup => kupharigolu, "gopherwood".

> > > > > Tegere, targa,
> > > > >
> > > > > Note: cf Mbabaram & Zulu term for wood shield vs wicker roundshield
> > > > > -
> > > > >
> > > > > MacGregor 1889
> > > > > New Guinea
Ed. DD

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xyambuatlaya

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On Mon, Nov 19, 2018, 8:25 PM Daud Deden <daud.deden@gmail.com> wrote:

From whence the cubical form so common today? Stone blocks of pyramids & castle walls, bricks in ziggurats, apparently started at the same place that flatbread was made.

Papuans encountered giant wombats in Australia, plausibly while paddling their new sago palm rind canoes.

Wombats are the only animals on Earth that excrete cubical feces, iow, they poop cubes, which they sometimes stack to attract the opposite sex.

The oldest ground-stone axes are from coastal Northern Australia.

An interesting convergence.

https://www.bbc.com/news/world-australia-46258616

Manure is widely used in India etc. in making clay bricks, adobe huts, flooring & walls, giving tensile strength. The Indus Valley civilization architecture featured sun-dried bricks. Did the design arrive with flat-bread, spatula-spade-paddles & canoes, ground axes, adzes, coconuts, bananas, sugar cane, via Papuan emigrés who eventually settled further west?

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xyambuatlaya

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So. Af. Caves redated

<http://dx.doi.org/10.1038/s41586-018-0711-0>


U­Pb-dated flowstones restrict South African early hominin record to dry
climate phases.
Robyn Pickering, Andy Herries, Jon Woodhead, John Hellstrom, Helen Green,
Bence Paul, Terrence Ritzman, David Strait, Benjamin Schoville & Phillip
Hancox 2018
Nature <https://www.nature.com/articles/s41586-018-0711-0.ris>

The Cradle of Humankind preserves a rich collection of fossil hominins
representing Australopithecus, Paranthropus & Homo.
The ages of these fossils are contentious, and have compromised the degree
to which the S.African hominin record can be used to test hypotheses of
human evolution.
But U­Pb analyses of horizontally bedded layers of CaCO3 (flow-stone)
provide a potential opportunity to obtain a robust chronology.
Flowstones are ubiquitous cave features, and provide a palaeo-climatic
context:
they grow only during phases of increased effective precipitation, ideally
in closed caves.

Here we show:
flowstones from 8 Cradle caves date to 6 narrow time-intervals between 3.2
& 1.3 Ma.
We use a kernel density estimate to combine 29 U­Pb ages into a single
record of flowstone growth intervals.
We interpret these as major wet phases:
an increased water supply, more extensive vegetation cover & at least
partially closed caves allowed for undisturbed semi-continuous growth of
the flowstones.
The intervening times represent substantially drier phases, during which
fossils of hominins & other fossils accumulated in open caves.
Fossil preservation, restricted to drier intervals, thus biases the view
of hominin evolutionary history & behaviour,
it places the hominins in a community of comparatively dry-adapted fauna.
Although the periods of cave closure leave temporal gaps in the S.African
fossil record, the flowstones themselves provide valuable insights into
local & pan-African climate variability.
______

South Africa's hominin record is a fair-weather friend
21.11.18

New research from Robyn Pickering cs is the first to provide a timeline
for fossils from the caves within the Cradle of Humankind.
It also sheds light on the climate conditions of our earliest ancestors in
the area.
It corrects assumptions that the region's fossil-rich caves could never be
related to each other.
In fact, the research suggests fossils from Cradle caves date to just 6
specific time-periods.

Robyn Pickering:
"Unlike previous dating work (which often focused on 1 cave, sometimes
even just 1 chamber of the cave), we are providing
- direct ages for 8 caves &
- a model to explain the age of all the fossils from the entire region.
Now we can link together the findings from separate caves, and create a
better picture of evolutionary history in S-Africa."

The Cradle is a World Heritage Site, made up of complex fossil-bearing
caves.
It's the world's richest early hominin site, home to nearly 40 % of all
known human ancestor fossils (e.g. Au.africanus "Mrs Ples").

Using U-Pb dating, researchers analysed 28 flow-stone layers, found
sandwiched between fossil-rich sediment in 8 caves across the Cradle:
the fossils in these caves date to 6 narrow time-windows between 3.2 & 1.3
Ma:
"The flowstones are the key.
We know they can only grow in caves during wet times, when there is more
rain outside the cave.
By dating the flowstones, we are picking out these times of increased
rainfall.
We therefore know that during the times in between, when the caves were
open, the climate was drier, more like what we currently experience."

This means the early hominins living in the Cradle experienced big changes
in local climate, from wetter to drier conditions, at least 6 times
between 3 & 1 Ma,
but only the drier times are preserved in the caves, skewing the record of
early human evolution.

Up until now, the lack of dating methods for Cradle fossils made it
difficult to understand the relationship between E & S.African hominin spp.
The S.African record has often been considered undateable, compared to
E.Africa, where volcanic ash layers allow for high resolution dating.

Andy Herries, co-author:
"the S.African record was the first to show Africa as the origin point for
humans,
but the complexity of the caves & difficultly dating them has meant that
the S.African record has remained difficult to interpret.
In this study, we show that the flow-stones in the caves can act almost
like the volcanic layers of E.Africa, forming in different caves at the
same time, allowing us to directly relate their sequences & fossils into a
regional sequence."

Pickering began dating the Cradle caves in 2005, as part of her PhD
research.
This new publication is the result of 13 years of work.
The results return the Cradle to the forefront, and open new opportunities
to answer complex questions about human history in the region.

Bernard Wood, no co-author:

"Robyn cs have made a major contribution to our understanding of human
evolution.
This is the most important advance to be made since the fossils were
discovered.
Dates of fossils matter a lot.
The value of the S-African evidence has been increased many-fold by this
exemplary study of its temporal and depositional context."

https://archaeologynewsnetwork.blogspot.com/2018/11/south-africas-hominin-r
ecord-is-fair.html#jP5tdY208yUv22yV.99

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xyambuatlaya

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Beer & bread

DDeden
to me
5 minutes agoDetails
Hymn to Ninkasi, god of beer

Bappir@Sum: flatbread, pita pan naan roti brod

You handle the dough, mix with shovel/spade/paddle/spatula in a pit, the bappir (barley flat bread) with date honey. You bake it in big oven, order the hulled grain piles, water the malts on the ground, then soak it in a jar, waves rise then fall, then spread the cooked mash on reed mats to cool, then hold the sweet wort brewed with honey & wine, and filter/sieve/sift into the collecting vat, then pour out the filtered beer like the onrushing Tigris & Euphrates.

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xyambuatlaya

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