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Out-of-India - From Theory to Truth: Part 2

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Nilesh Oak
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Re: Out-of-India - From Theory to Truth: Part 2

Postby Nilesh Oak » 05 Jun 2016 17:28

Shiv writes...

Thanks Rajesh. Every time I start editing my work - I feel dissatisfied with the completeness of some things and am simply trying to learn more. And in the meantime a lot of new genetics material has appeared - but that is less of a problem - that can be included fairly easily.


One (humble) suggestion is to partition them into few and bring out first portion of it as a ...either cohesive theme by itself (and thus a stand alone book) or volume 1 of the series.

Someone wrote that as soon as one presses the 'publish' button, an author realizes immediately how s/he would re-write 80% of what s/he just published. I can tell my from two data points that this is literally and figuratively true!

Another thing to watch for is that we may put too much into one book. I certainly did and thus it is very dense (to some...not all). I was not sure if I would ever publish (or will have time to publish) anything else after that one attempt (When did the Mahabharata War happen?) and thus wanted to insert as much as of my original research into it. Even then, some 70%+ I could not include in the book.

On multiple occasions, few academics who have read my work (Mahabharata war) have told me that the material it contains would fill 'at least 5 quality PhD dissertations.

Only my $0.02

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Re: Out-of-India - From Theory to Truth: Part 2

Postby vishvak » 05 Jun 2016 17:39

History seems to be consensus concoction, like Wikipedia where whatever the in-vague credible source of the day says - here exotic subjects like written phonetics, Indology, etc - becomes the printed word. If this is disclosed to students already, may be the subject will become much more interesting and scoring even for the most disinterested student.

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Re: Out-of-India - From Theory to Truth: Part 2

Postby sudarshan » 05 Jun 2016 18:45

An uncomfortably large part of history is plain fiction. Authors who research "history" in order to write historical fiction, sooner or later stumble into this disconcerting fact. It's mostly "he said/ she said." If the he or she who said it is credible, and is also listened to by the people of the time, then we have some meaningful data. The most dangerous sources are the ones who have some kind of bias or agenda, but who maintain this veneer of credibility. Sometimes they do this by being the first movers or only movers in fields which nobody else is interested in. So they get away with saying "I spent half my life studying this field - what are *your* credentials?" And the other guy who has no interest in researching the field in the first place, just backs off, leaving the first guy with the tag of "expert in the field." Here's a thought - why not respond - "I spent half my life studying the psychology of biased sources and researchers, including you???"

Europeans of the colonial age had the further advantage of having a consistent bias, regardless of the "researcher." IOW, they all had a shared interest in portraying the orient in a certain way. Now it's an uphill task to unravel their agendas and display the bias, even to Indians themselves :roll:. This is true not just of oriental studies and Indology, but of Christianity and Islam itself. But that's another couple-a cans of worms entirely.

But there is hope :). Keep hammering at the biases and dragging them into the daylight, and it will eventually sink in with a new generation - the old fogies (no insult intended to older people, but a lot of insult is very much intended to fogies) will never change. For instance - Freud would today be regarded as *the expert* in psychology, if Jung, his disciple, had not come up with his own theories in opposition to Freud. Since Jung did this not too long after Freud came up with his theories, the same generation which Freud addressed, got to see that Freud wasn't such an unchallenged expert after all. Now since we are so many generations away from the prime movers of the European fiction-masquerading-as-history age, we just have to use the advantage we have, which is, that we don't care what the intervening generations thought, or even what the current generation thinks, but we are darn-well going to address the coming generations, over which those Europeans have no control.

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Re: Out-of-India - From Theory to Truth: Part 2

Postby gandharva » 05 Jun 2016 21:11

Nilesh Oak wrote:
gandharva wrote:Link for pdf of the book by Jatindra Mohan Chaterjie. I downloaded all JPGs from that Avesta.org link and converted to pdf. :D

https://www.dropbox.com/s/xh0mqaby120rd ... 3.pdf?dl=0

Gandharva ji,

I can not thank you enough. Thanks also to Shiv, AGupta and JE Menon ji.


Nilesh ji, i edited the download link for reloaded pdf file in my post. I am posting that link here as well for your convenience.

https://drive.google.com/open?id=0B2rmZ ... k5fNzRYRkk

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Re: Out-of-India - From Theory to Truth: Part 2

Postby gandharva » 08 Jun 2016 02:30

Indian genetic history in three simple graphs

Enjoy, but please, those of you still sore about the passing of the Out of India, Out of Armenia, Out of Your Hat, or indeed, Out of Your Ass Indo-European hypotheses, try not to fill up the comments with the usual inane drivel. Thanks in advance for your cooperation.
http://eurogenes.blogspot.ca/2016/05/in ... imple.html
Image

Image

Image



What Gurus have to say about abv?

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Re: Out-of-India - From Theory to Truth: Part 2

Postby ramana » 08 Jun 2016 04:41

svinayak wrote:
shiv wrote: Guess how a Frenchman would pronounce "Zend"? du Perron's work was rejected until someone found the 13 century record of a 10th century Persian text written by a Parsi Sanskrit scholar (Neryosang Dhaval) on which linguists did their reconstructions, creating a language called "Avestan" from the name "Zend Avesta"

These linguists created a land called Avesta from the French name of a book and created people called Avestans, just like they created people called Aryans from the word "Arya" .


All the colonial historians have the same record. This concoction of people, language and history was targetted towards the people in Europe understand this part of the world. The European elite, universities and monarchies read these historians and imagined the people of the east.
This continued in the 20th century and in case of Indian subcontinent the baggage of sociology, indology narratives continued to the present day universities. Indian leftist historians took it from where it was left before and expanded it to the minds of the new Indian generation.



I saw a painting in the Louvre a couple of weeks ago titled Coramandel. The people depicted were Chinese!!! It was painted in 18th century.

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Re: Out-of-India - From Theory to Truth: Part 2

Postby shiv » 08 Jun 2016 07:39

gandharva wrote:Indian genetic history in three simple graphs

Enjoy, but please, those of you still sore about the passing of the Out of India, Out of Armenia, Out of Your Hat, or indeed, Out of Your Ass Indo-European hypotheses, try not to fill up the comments with the usual inane drivel. Thanks in advance for your cooperation.

:rotfl:

Interesting. The author is upset enough about people claiming OIT to make the comment he has made at the start. It indicates anger and irritation and a desperate attempt to convince someone that they are wrong. I am happy to see that emotion. It is, after all the exact mirror image of the emotion felt by people who see the fakeness of the Aryan Invasion theory. Even if OIT is totally wrong it is well worth pursuing that line simply to irritate and obfuscate and do to others what the racist AITians did to Indians.


As regards the genetic data - there is nothing new. It has all been discussed here before, - some of it very early on., The Munda speaker genes coming from the East was discussed 2-3 years ago in the context of Witzels totally fake "para Munda" speaker theory where he claimed that Harappa was full of cooked up language "ParaMunda" speakers. Actually in India, Munda speaker genes are found only East of Bihar and nowhere near Harappa. Munda speaker mythology includes fights against Asuras - and you know which side they are on.

The Z93 stuff is the same - as is the statement about ASI/ANI mix, But there are two-three things missing - which may be significant in this debate

1.Z93 occurs only in 10% Indian males (If I remember right) What about the other 90%?
2. Everyone gets orgasms by talking about corded ware. How come there is no reference to Indus Valley artefacts found in middle east and BMAC?
3. How did upper caste in North India and Afghanistan for that matter get Chenchu and Onge genes?

Everyone has his biases so seeing people get angry makes the OIT idea delicious - never mind the truth. That Blog author has his chaaddis in a tight knot. Cheers to that

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Re: Out-of-India - From Theory to Truth: Part 2

Postby A_Gupta » 14 Jun 2016 05:25

I think we need to understand errors in DNA sequencing.
Especially with SNPs.
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3593722/

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Re: Out-of-India - From Theory to Truth: Part 2

Postby A_Gupta » 18 Jun 2016 22:25

Batch effects in high volume data.
http://www.nature.com/nrg/journal/v11/n ... g2825.html
High-throughput technologies are widely used, for example to assay genetic variants, gene and protein expression, and epigenetic modifications. One often overlooked complication with such studies is batch effects, which occur because measurements are affected by laboratory conditions, reagent lots and personnel differences. This becomes a major problem when batch effects are correlated with an outcome of interest and lead to incorrect conclusions. Using both published studies and our own analyses, we argue that batch effects (as well as other technical and biological artefacts) are widespread and critical to address. We review experimental and computational approaches for doing so.

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Re: Out-of-India - From Theory to Truth: Part 2

Postby A_Gupta » 20 Jun 2016 17:22

A new challenge:
http://biorxiv.org/content/early/2016/06/16/059311
The genetic structure of the world's first farmers

In South Asia, our dataset provides insight into the sources of Ancestral North Indians (ANI),
a West Eurasian related population that no longer exists in unmixed form but contributes a variable amount of the ancestry of South Asians (Supplementary Information, section 9) (Extended Data Fig. 4). We show that it is impossible to model the ANI as being derived from any single ancient population in our dataset. However, it can be modelled as a mix of ancestry related to both early farmers of western Iran and to people of the Bronze Age Eurasian steppe; all sampled South Asian groups are inferred to have significant amounts of both ancestral types. The demographic impact of steppe related populations on South Asia was substantial, as the Mala, a south Indian population with minimal ANI along the ‘Indian Cline’ of such ancestry is inferred to have ~18% steppe-related ancestry, while the Kalash of Pakistan are inferred to have ~50%, similar to present-day northern Europeans

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Re: Out-of-India - From Theory to Truth: Part 2

Postby Prem Kumar » 21 Jun 2016 09:52

Look at Figure 2, Page 28 of the PDF copy of this paper. The "ancient populations" are all Europe or close enough to it: Steppe, Anatolian, European, Armenian, Central Hunter Gatherer (CHG), EHG etc. The rest of the "ancient populations" don't exist or don't count. Somehow, the Harappan civilization, that started in 8000 BCE, doesn't qualify as "ancient population".

Iran is now included in the European White Boys club. Congrats Iran!

What we are seeing in genetics is a redux of what linguistics was, since the 19th century:

Phase 1: An initial hypothesis, with selectively picked and wrong data is woven into a theory
Phase 2: A lot of subsequent work is produced to support this flimsy theory by usage of mutually referencing data (a.k.a circle-jerk). Volume of work is important in this phase. The volume should support the narrative. Contrary data is ignored.
Phase 3: When enough "scholarly work" is thus produced, the hypothesis is assumed to be "proven", with no need for any further proof. There is a heavy burden of proof on any competing theory. This directly goes against the very spirit of science, because in science, no theory is ever "proved correct". A theory is only 1 experiment or data-point away from being proved wrong.

This is what Rajiv Malhotra calls a hegemonic discourse.

Genetics is getting there: albeit slowly, because its a bit more scientific. So, there are contrarian voices, especially from places like CCMB. But its a double edged sword. Precisely because genetics is supposed to be "more scientific", once a hegemonic discourse on genetics gets built up, it lends greater legitimacy to theories like "Steppe ancient DNA". It needs to be fought more vigorously. Indian geneticists must shed their diffidence and boldly call out the Steppe quakery.

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Re: Out-of-India - From Theory to Truth: Part 2

Postby A_Gupta » 21 Jun 2016 15:38

Well, the ancient populations are wherever ancient DNA has been recovered.

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Re: Out-of-India - From Theory to Truth: Part 2

Postby Nilesh Oak » 21 Jun 2016 16:33

Prem Kumar wrote:
What we are seeing in genetics is a redux of what linguistics was, since the 19th century:

Phase 1: An initial hypothesis, with selectively picked and wrong data is woven into a theory
Phase 2: A lot of subsequent work is produced to support this flimsy theory by usage of mutually referencing data (a.k.a circle-jerk). Volume of work is important in this phase. The volume should support the narrative. Contrary data is ignored.
Phase 3: When enough "scholarly work" is thus produced, the hypothesis is assumed to be "proven", with no need for any further proof. There is a heavy burden of proof on any competing theory. This directly goes against the very spirit of science, because in science, no theory is ever "proved correct". A theory is only 1 experiment or data-point away from being proved wrong.

This is what Rajiv Malhotra calls a hegemonic discourse.

Genetics is getting there: albeit slowly, because its a bit more scientific. So, there are contrarian voices, especially from places like CCMB. But its a double edged sword. Precisely because genetics is supposed to be "more scientific", once a hegemonic discourse on genetics gets built up, it lends greater legitimacy to theories like "Steppe ancient DNA". It needs to be fought more vigorously. Indian geneticists must shed their diffidence and boldly call out the Steppe quakery.


Excellent summary.

Here is my framework for classifying works ( I had Archeo-astronomy and Archeology in mind while developing it, but is expected to be applicable anywhere).

https://nileshoak.wordpress.com/2016/06 ... on-part-3/
--

Am reading biography of Prof. B B Lal (Archeologist) and in spite of his tremendous work (He is 90+), how he drew inferences (based on his findings) for the timing of ancient Indian events leaves much to be desired.

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Re: Out-of-India - From Theory to Truth: Part 2

Postby csaurabh » 21 Jun 2016 16:39

There is a Hrithik Roshan film called 'Mohenjo-daro' to be released shortly.

As far as info I can find, it is pure fantasy. No references to Aryans or Dravidians.

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Re: Out-of-India - From Theory to Truth: Part 2

Postby shiv » 21 Jun 2016 16:55

A_Gupta wrote:A new challenge:
http://biorxiv.org/content/early/2016/06/16/059311
The genetic structure of the world's first farmers

In South Asia, our dataset provides insight into the sources of Ancestral North Indians (ANI),
a West Eurasian related population that no longer exists in unmixed form but contributes a variable amount of the ancestry of South Asians (Supplementary Information, section 9) (Extended Data Fig. 4). We show that it is impossible to model the ANI as being derived from any single ancient population in our dataset. However, it can be modelled as a mix of ancestry related to both early farmers of western Iran and to people of the Bronze Age Eurasian steppe; all sampled South Asian groups are inferred to have significant amounts of both ancestral types. The demographic impact of steppe related populations on South Asia was substantial, as the Mala, a south Indian population with minimal ANI along the ‘Indian Cline’ of such ancestry is inferred to have ~18% steppe-related ancestry, while the Kalash of Pakistan are inferred to have ~50%, similar to present-day northern Europeans

This paper gets many of its conclusions from the following statement
The ‘Basal Eurasians’ are a lineage hypothesized 13 to have split off prior to the differentiation
of all other Eurasian lineages, including both eastern non-African populations like the Han
Chinese, and even the early diverged lineage represented by the genome sequence of the
~45,000 year old Upper Paleolithic Siberian from Ust’-Ishim 11

Dates (at first glance) appear to be 10,000 yrs ago

The "basal European Population" theory comes from this paper (ref 13 above paper)
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4170574/
We model these populations’ deep relationships and show that early European farmers had ~44% ancestry from a ‘basal Eurasian’ population that split before the diversification of other non-African lineages.


All in all - not much of a paper to say anything..hypothesis based on earlier hypothesis


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Re: Out-of-India - From Theory to Truth: Part 2

Postby ramana » 21 Jun 2016 19:58

Good was just about to suggest putting it on Twitter to spread awareness.

If the conclusions of this seminal paper are based on hypothesis of earlier paper isn't this piling on shaky grounds?

How did David Reich lend his name to this 64 author concoction?
What is his credibility/

Is he another new age Maxmueller of genetics?

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Re: Out-of-India - From Theory to Truth: Part 2

Postby Prem Kumar » 22 Jun 2016 00:03

I had earlier posted about this Reich character & why I think he is a snake. His name shows up in CCMB papers too. I think he is Priya Moorjani's advisor. Runs with the hare & hunts with the hounds. You can always find a soundbite from him even on articles based on papers where the 1st author is Moorjani, Thangaraj or others (presumably because he is white and they are not)

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Re: Out-of-India - From Theory to Truth: Part 2

Postby Prem » 22 Jun 2016 00:22

http://www.businessinsider.com/angkor-w ... dar-2016-6
( River of 1000 Lingas in Cambodia, Near Angkor Wat)

Scientists have discovered an ancient city that may be a terrible omen for modern civilizationIt's a monumental discovery, based on two major archaeological surveys of the area around Siem Reap, not far from the famous temple complex of Angkor Wat in the heartlands of the ancient Khmer culture.Once, an archaeologist would have spent their entire career hacking through the jungle, machete in hand, in order to map these ruins.But thanks to the clever use of airborne laser scanning technology, the entire project took just three years. Such is the incredible power of Lidar - short for "light detection and ranging" - an innovation which is causing great excitement throughout the archaeological world.From 2012 to 2015, archaeologist Damian Evans and his team used Lidar technology, mounted on helicopters, to map some 2,230 square kilometers (862 square miles) with an accuracy of +/- 150 mm (6 inches).With 16 data points measured every square meter, the researchers were not only able to pinpoint well-known monumental stone structures in exquisite detail, they also discovered the massive urban cultures which surrounded these temples, identifiable by the remains of earthworks such as mounds, canals, roads and quarries.

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Re: Out-of-India - From Theory to Truth: Part 2

Postby A_Gupta » 22 Jun 2016 05:51

This following is about cattle, not humans. But I found it counterintuitive. Shiv, can you explain why this plot is so variegated?

http://biorxiv.org/content/biorxiv/earl ... 9.full.pdf
"Population Structure Analysis of Globally Diverse Bull Genomes" has this fascinating plot.

Among these genomes, there are m = 3,967,995 single nucleotide polymorphisms (SNPs) with no missing values and minor allele frequencies ¿ 0.05 (Supplementary Fig. 2). To explore structural complexity, whole genome sequences of n = 432 selected samples were hierarchically clustered using Manhattan distances (Figure 3, colored by 13 different breeds). It is evident that official breed codes (or countries of origin) do not necessarily represent the genetic diversity among bulls represented by SNPs.


Image

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Re: Out-of-India - From Theory to Truth: Part 2

Postby shiv » 22 Jun 2016 06:14

A_Gupta wrote:This following is about cattle, not humans. But I found it counterintuitive. Shiv, can you explain why this plot is so variegated?

Could this sentence be the explanation?
Based on observing a largely continuous genetic spectrum compared to breeds, we demonstrated that breeds do not account for structural complexity. We speculate that many cattle breeds, including presumed founders, are not as isolated or discrete as one would be led to believe.

That is, although breeds have different names they are all related?

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Re: Out-of-India - From Theory to Truth: Part 2

Postby A_Gupta » 22 Jun 2016 06:26

The breeds are certainly related.

What is a breed? Is there really such a thing as a purebred?

Let's begin by defining what a breed is. The late Hilton Briggs, the quintessential authority on breeds and author of the book, “Modern Breeds of Livestock,” defined a breed as: “a group of animals that, as a result of breeding and selection, have certain distinguishable characteristics.”

Briggs goes on to define a purebred animal as “an individual both of whose parents are duly registered in a Registry Association.”

It's interesting to note that Briggs says nothing about “breed purity” or “percentage of blood” in either definition. If one delves back into livestock history, it can be concluded that very few populations of so-called “purebred” cattle existed. Rather, nearly all breeds were developed by combining various strains of cattle within a region into a generally agreed-upon type.


http://beefmagazine.com/mag/beef_breed

I think a cattle generation is about 2 years; and I had thought that sufficient generations would have passed in jaati endogamy that the cross-lineage diversity would have been greatly diluted and be invisible. How is it that humans fall into neat trees but cattle breeds do not?

PS:
I'm interested in understanding when structure is real and when it is an artifact. E.g.,
http://arunsmusings.blogspot.com/2016/0 ... lines.html

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Re: Out-of-India - From Theory to Truth: Part 2

Postby shiv » 22 Jun 2016 07:09

A_Gupta wrote:
I think a cattle generation is about 2 years; and I had thought that sufficient generations would have passed in jaati endogamy that the cross-lineage diversity would have been greatly diluted and be invisible. How is it that humans fall into neat trees but cattle breeds do not?

:D
Question is, do humans from restricted geographic groups fall into neat trees? I don't think Indians fall into neat trees, although when compared to Europeans, 'Eurasians", far east peoples the trees become apparent. I doubt if it would be possible to put Bengalis and Maharashtrians in separate trees. But they look and speak different and are from places as far apart as Italy and the UK

With cattle there probably has been constant exchange of population so that "Breeds" might seem different but are genetically more "united" than appears to be the case.

I mean seriously - are these even different "countries"? They may have "breeds" but its the same damn area with constant population exchange,

Australia, Austria, Canada, Denmark, Finland, France, Germany,
Italy, Netherlands, New Zealand, Norway, Spain, Sweden, Switzerland, United Kingdom, and United States


Australia and New Zealand have been populated with European species. Probably USA and Canada as well.

That aside I don't think the "number of generations" gives rise to genetic differentiation as much as the passage of time - which is what leads to mutation, expression of that mutation (if it is not fatal) and expansion of a population with that mutation. However very fast breeding species (eg Viruses and bacteria) tend to show up mutations sooner. But I don't think even Fruit flies and rats show up genetic variation sooner than a century or two - which is longer than the study of genetics has been in existence

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Re: Out-of-India - From Theory to Truth: Part 2

Postby A_Gupta » 22 Jun 2016 07:29

shiv wrote:That aside I don't think the "number of generations" gives rise to genetic differentiation as much as the passage of time - which is what leads to mutation, expression of that mutation (if it is not fatal) and expansion of a population with that mutation. However very fast breeding species (eg Viruses and bacteria) tend to show up mutations sooner. But I don't think even Fruit flies and rats show up genetic variation sooner than a century or two - which is longer than the study of genetics has been in existence


Each time DNA is copied there is an error rate in copying - of the order of 1 per 10^8 base pairs in humans. Of course, the only errors that matter are those that can be inherited. Hence the number of generations is what counts. (The error rate might vary somewhat among human populations by up to a factor of 2 - that is what has been found so far.)

100 human generations might be 2500 years. 100 cow generations could be as little as 200 years. If breed endogamy is practiced for "pure breeds", if cattle breeds are of the order of a couple of hundred years old, and if error rates in DNA copying are similar to humans, then why won't they show structures analogous to all those supposedly real plots of Indian tribes and castes?

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Re: Out-of-India - From Theory to Truth: Part 2

Postby shiv » 22 Jun 2016 07:48

A_Gupta wrote:Each time DNA is copied there is an error rate in copying - of the order of 1 per 10^8 base pairs in humans. Of course, the only errors that matter are those that can be inherited. Hence the number of generations is what counts. (The error rate might vary somewhat among human populations by up to a factor of 2 - that is what has been found so far.)

100 human generations might be 2500 years. 100 cow generations could be as little as 200 years. If breed endogamy is practiced for "pure breeds", if cattle breeds are of the order of a couple of hundred years old, and if error rates in DNA copying are similar to humans, then why won't they show structures analogous to all those supposedly real plots of Indian tribes and castes?


I am no geneticist - merely a person with some interest and a little knowledge. That said:

The real problem is that an error in any random cell makes no difference
1. The error has to be in a cell that is reserved for species propagation (specific cells in the testis/ovary)
2. No one knows how many errors end in death. Failed pregnancies "Had sex but did not get pregnant" or a spontaneous abortion could be more frequent than we know and could be because of these errors.
3. No one is completely sure (when I last read about this - quite a while ago)) about the extent to which DNA may be repaired and the mechanism by which genetic integrity is maintained over thousands of years.
4. Genes have not been completely mapped allowing people to pick up small changes from generation to generation

If 200 generations of cows are not showing the differences one expects, the premise about the number of generations needed to see change may be wrong. The statistic below is a guesstimate.
error rate in copying - of the order of 1 per 10^8 base pairs in humans

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Re: Out-of-India - From Theory to Truth: Part 2

Postby A_Gupta » 22 Jun 2016 16:46

^^^ One can chase down all the estimates, here's an example.

http://biorxiv.org/content/early/2016/06/17/059436
A direct multi-generational estimate of the human mutation rate from autozygous segments seen in thousands of parentally related individuals

"....1.45 ± 0.05 × 10^-8 per base pair per generation in autosomal coding sequence, with a corresponding non-crossover gene conversion rate of 8.75 ± 0.05 × 10^-6 per base pair per generation. This is at the lower end of exome mutation rates previously estimated in parent-offspring trios, "


For a genome-wide average mutation rate, the direct approaches have consistently estimated a rate of 1-1.25 × 10^-8 per base pair (bp) per generation, significantly lower than phylogenetic estimates, which suggest around ~2 × 10^-8 per bp per generation or estimates from population-genetic methods which suggest 1.6-1.7 × 10^-8 per bp per generation.

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Re: Out-of-India - From Theory to Truth: Part 2

Postby shiv » 22 Jun 2016 18:08

A_Gupta wrote:^^^ One can chase down all the estimates, here's an example.

Don't know. Please expand on what you are getting at. What are you looking for?

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Re: Out-of-India - From Theory to Truth: Part 2

Postby A_Gupta » 22 Jun 2016 19:16

On a different line of attack, but related:
http://www.ncbi.nlm.nih.gov/pmc/article ... figure/F3/

The caption reads: "Conveniently defined metapopulations that mask human evolutionary history and relationships (adopted from Zhivotovsky et al., 2003, Figure 6). This tree is simply instrumentally produced to meet the demand of our interest in continental groups/human races and may function under some circumstances as useful problem-solving tool. However, from an evolutionary perspective, it carries no natural meaning or independent reality. [“Reduced population tree showing four separation events”] (Zhivotovsky et al., 2003). Figure reproduced with permission from Cell Press/Elsevier."

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Re: Out-of-India - From Theory to Truth: Part 2

Postby ramana » 22 Jun 2016 20:03

Prem Kumar wrote:I had earlier posted about this Reich character & why I think he is a snake. His name shows up in CCMB papers too. I think he is Priya Moorjani's advisor. Runs with the hare & hunts with the hounds. You can always find a soundbite from him even on articles based on papers where the 1st author is Moorjani, Thangaraj or others (presumably because he is white and they are not)



In the modern field of Aryan genetics, this David Reich is like Wendy Doniger of the AIT and needs to be taken down.

He might be a fine person and a great geneticist but he is suing his knowledge for propagating race theory which is antediluvian.

I bet its not science that is driving his research.

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Re: Out-of-India - From Theory to Truth: Part 2

Postby A_Gupta » 23 Jun 2016 04:58

Reich:
https://genetics.med.harvard.edu/reich/ ... lcome.html

From there:
Massive migration from the steppe was a source for Indo-European languages in Europe”

(Link to PDF: https://genetics.med.harvard.edu/reich/ ... e14317.pdf )

The supplementary reading (Supplement 11) which is at the end of a 30 MB download is worth reading.
(found somewhere on this page: http://www.nature.com/nature/journal/v5 ... 14317.html )

The upshot is that since they have ancient European DNA from various eras, they can say that there was a major influx of early farmers from Anatolia into Europe around 8000-7000 years ago; and there was a major migration from the steppe into Europe around 5000-4500 years ago. "...these migrants acconted for at least 3/4 of the ancestry of the Corded Ware people in Germany and much of the ancestry of other Late Neolithic/Bronze Age populations of Germany and present-day northern Europeans".

"Thus, the main argument in favor of
the Anatolian hypothesis (that major language change requires major migration) can now also be
applied to the Steppe hypothesis. While we cannot go back in time to learn what languages the
migrants spoke, it seems more likely than not that the Corded Ware people we sampled spoke the
languages of the people who contributed the great majority of their ancestry (Yamnaya), rather than
the local languages of the people who preceded them. Thus, our results increase the plausibility that
the Corded Ware people and those genetically similar groups who followed them in central Europe
spoke a steppe-derived Indo-European language. More generally, our results level the playing field
between the two leading hypotheses of Indo-European origins, as we now know that both the Early
Neolithic and the Late Neolithic were associated with major migrations."

"However, we can definitely reject that the breakup of Indo-European occurred as late as 4000 years ago, as by ~4500 years ago the migration into Europe had already taken place. Moreover, this migration clearly resulted in a large population turnover, meaning that the Steppe hypothesis does not require elite dominance to have transmitted Indo-European languages into Europe. Instead, our
results show that the languages could have been introduced simply by strength of numbers:
via major migration in which both sexes participated".

---- My note - the older date I think starts creating problems for the traditional historical linguists' clocks.

"The Anatolian hypothesis becomes less plausible as an explanation for the origin of all Indo-
European languages in Europe, as it can no longer claim to correspond to the only major
population transformation in European prehistory, and it must also account for the language
of the steppe migrants. However, the Anatolian hypothesis cannot be ruled out entirely by our
data, as it is possible that it still accounts for some of the major branches of the Indo- European language family in Europe, especially the branches of the south where the proportion of steppe ancestry today is smaller than in central and northern Europe".

"An important caveat to using ancient DNA to make arguments about the origins of languages is that
prior to the invention of writing, we have no way to directly tie ancient cultures to a language.
Nevertheless, by establishing that major migrations or exchanges of genes occurred, we identify
movements of people that would have been plausible vectors for the spread of languages, and we can
establish some periods in time as the most plausible ones for language spread. Thus, genetic data can
change the balance of probabilities among competing hypotheses as we outline above."


"It is still possible that the steppe migration detected by our study into Late Neolithic Europe might account for only a subset of Indo-European languages in Europe, and other Indo-European languages arrived in Europe not from the steppe but from either an early “Neolithic Anatolian” or later “Armenian plateau” homeland."

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Re: Out-of-India - From Theory to Truth: Part 2

Postby A_Gupta » 23 Jun 2016 06:21


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Re: Out-of-India - From Theory to Truth: Part 2

Postby shiv » 23 Jun 2016 07:29

A_Gupta wrote:Reich:
https://genetics.med.harvard.edu/reich/ ... lcome.html

From there:
Massive migration from the steppe was a source for Indo-European languages in Europe”

(Link to PDF: https://genetics.med.harvard.edu/reich/ ... e14317.pdf )

The supplementary reading (Supplement 11) which is at the end of a 30 MB download is worth reading.
(found somewhere on this page: http://www.nature.com/nature/journal/v5 ... 14317.html )

"However, we can definitely reject that the breakup of Indo-European occurred as late as 4000 years ago, as by ~4500 years ago the migration into Europe had already taken place. Moreover, this migration clearly resulted in a large population turnover, meaning that the Steppe hypothesis does not require elite dominance to have transmitted Indo-European languages into Europe. Instead, our
results show that the languages could have been introduced simply by strength of numbers:
via major migration in which both sexes participated".

---- My note - the older date I think starts creating problems for the traditional historical linguists' clocks.

Thanks for da link. Didja see this?
haplogroups R1a and R1b were found in 60% of Late Neolithic/Bronze Age Europeans outside Russia (n10), and in 100% of the samples from European Russia from all periods (7,500–2,700BC;n 59). R1a and R1b are the most common haplogroups in many European populations today18,19,and our results suggest that they spread into Europe from the East after 3,000BC.

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Re: Out-of-India - From Theory to Truth: Part 2

Postby gandharva » 25 Jun 2016 06:39

"Finally, the latest whole ancient genome studies indicated that both modern European and Indian populations (with a north-south gradient) are on an average closer to ancient steppe populations than they are to each other. This would mean that populations related to the ancient steppe populations them contributed to the ancestry of both the Indians and Europeans via admixture with unrelated local groups."

https://manasataramgini.wordpress.com/2 ... europeans/

Is abv colored part true?

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Re: Out-of-India - From Theory to Truth: Part 2

Postby shiv » 25 Jun 2016 08:19

gandharva wrote:"Finally, the latest whole ancient genome studies indicated that both modern European and Indian populations (with a north-south gradient) are on an average closer to ancient steppe populations than they are to each other. This would mean that populations related to the ancient steppe populations them contributed to the ancestry of both the Indians and Europeans via admixture with unrelated local groups."

https://manasataramgini.wordpress.com/2 ... europeans/

Is abv colored part true?

I am sure it is true. That is what has been shown in the paper linked a few posts above yours by AGupta. You did not have to go the manasataramgini's blog to discover that.

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Re: Out-of-India - From Theory to Truth: Part 2

Postby RajeshA » 25 Jun 2016 10:26

gandharva wrote:"Finally, the latest whole ancient genome studies indicated that both modern European and Indian populations (with a north-south gradient) are on an average closer to ancient steppe populations than they are to each other. This would mean that populations related to the ancient steppe populations them contributed to the ancestry of both the Indians and Europeans via admixture with unrelated local groups."

https://manasataramgini.wordpress.com/2 ... europeans/

Is abv colored part true?


If the ancient Steppe population is a half-way house between Indics and Euros, it would be true. I would imagine that ANI differentiated into many groups in North India and Central Asia, whereas the North Indian groups continued to develop civilizationally, northern Central Asian groups continued to remain nomadic and simplistic, and basically became net cultural importers from ANI groups further south in North India, who had in the meantime fused with ASI groups. It was the cultural mixing between the ANI and ASI that gave the groups in North India their cultural leap forwards. The Central Asian groups profited from this cultural progress and took it along with them as they spread through Eurasia.
,
It is the non-mixed North Indian ANI and mixed ANI-ASI that influenced the unmixed Central Asian ANI, rather than some culturally isolated Central Asian ANI that gave rise to Europeans and Indians after mixing with ASI, as they spread around.

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Re: Out-of-India - From Theory to Truth: Part 2

Postby shiv » 25 Jun 2016 21:17

RajeshA wrote:If the ancient Steppe population is a half-way house between Indics and Euros, it would be true. I would imagine that ANI differentiated into many groups in North India and Central Asia, whereas the North Indian groups continued to develop civilizationally, northern Central Asian groups continued to remain nomadic and simplistic, and basically became net cultural importers from ANI groups further south in North India, who had in the meantime fused with ASI groups. It was the cultural mixing between the ANI and ASI that gave the groups in North India their cultural leap forwards. The Central Asian groups profited from this cultural progress and took it along with them as they spread through Eurasia.
,
It is the non-mixed North Indian ANI and mixed ANI-ASI that influenced the unmixed Central Asian ANI, rather than some culturally isolated Central Asian ANI that gave rise to Europeans and Indians after mixing with ASI, as they spread around.

There was a reason for my posting the following quote from the same paper that was mentioned earlier by AGupta and brought up again as a quote from Manasataramgini's blog
haplogroups R1a and R1b were found in 60% of Late Neolithic/Bronze Age Europeans outside Russia (n10), and in 100% of the samples from European Russia from all periods (7,500–2,700BC;n 59). R1a and R1b are the most common haplogroups in many European populations today18,19,and our results suggest that they spread into Europe from the East after 3,000BC.


It is wrong to assume that migration was only in one direction, either into India or out of India, or into steppe or out of steppe. These genetics papers speak only of what has been found and all sorts of disparate things have been found

For example (recalling from memory) - R1a is found in upto 10% of Scandinavians and in 30% Indians.R1a extends from India to Europe and that is why it attracts so much attention as a connection to "Indo-European" (previously called Indo-Aryan) languages

Now here it gets interesting.

Let me list a few name-number combos that are related to Ria
From this paper by Underhill: http://www.nature.com/ejhg/journal/v23/ ... 1450a.html

We find in this paper a study of M417 (also called R1a1a1) which is a son of R1a. This M417 according to Underhill originated nearabout Iran 5800 years ago. M417 into 2 sons. One son - Z282 went to Europe. Another son, M93 went to India. If I recall right, M93 occurs in about 10% Indians (I need to check this). I will come to some of the other 90% in due course below

Now we look at another paper - linked several times above
http://arxiv.org/pdf/1502.02783.pdf - entitled "Massive migration from the steppe is a source for Indo-European languages in Europe"

This paper is a study of genes found in ancient preserved graves in Europe and Russia. Try and understand what it says.

haplogroups R1a and R1b were found in 60% of Late Neolithic/Bronze Age Europeans outside Russia (n 10), and in 100% of the samples from European Russia from all periods (7,500–2,700BC;n 9). R1a and R1b are the most common haplogroups in many European populations today 18,19, and our results suggest that they spread into Europe from the East after 3,000 BC

Explanation: I have mentioned above that R1a extends from India to Europe. But there is an R1b that occurs in Europe but not in India. Getting back to the paper mentioned above - the authors say that R1a and R1b were found in 60 ancient European graves (dead bodies in graves), and R1a and R1b were found in 100% of Russian graves from Yamnaya. Remember that name, Yamnaya. R1a and R1b are common in Europe today

The paper says that the Yamnaya grave combination of genes are older and they suddenly appeared in Europe 3000 years ago. That is why the paper says that language may have come from Russia/steppe/Yamnaya

So where do Yamnaya genes come from? The paper says:
Supplementary Information section 6), which implies that the Yamnaya have ancestry from popu-lations related to the Caucasus and South Asia
- note the South Asia

So I went and looked for the "Supplementary Information section 6" and this is what I got
http://arxiv.org/pdf/1502.02783.pdf
Massive migration from the steppe is a source for Indo-European languages in Europe

An interesting pattern occurs at K=8, with all the late LN/BA groups from central Europe and the Yamnaya having some of the “light green” component that is lacking in earlier European farmers and hunter-gatherers; this component is found at high frequencies in South Asian populations and its co-occurrence in late 56Neolithic/Bronze Age Europeans (but not earlier ones) and South Asians might reflect a degree of common ancestry associated with late Neolithic migratory movements (e.g., the ~5,800-year old TMRCA of Y-chromosome haplogroup R1a-M417 suggests some gene flow affecting both Europe and South Asia in this time frame11, although this date is subject to uncertainty due to poor estimates of the human mutation rate.)

At K=9 a European hunter-gatherer ancestral population (“dark blue”) appears; this was not present in an earlier analysis of the Human Origins modern populations and a much smaller number of ancient individuals2. The inclusion of a large number of ancient hunter-gatherers has probably caused such an ancestral population to appear in this analysis. European farmers now appear to be mixture of a Near Eastern (orange) and European hunter-gatherer (dark blue) ancestral populations, with an increase in the hunter-gatherer ancestry during the Middle Neolithic (reflecting the “resurgence” of such ancestryshown in PCA, Fig. 2a) and also during the Late Neolithic. Note, also, the persistent presence of the “light green” component that ties LN/EBA groups to South Asia between K=9 and K=15. A similar (darker green) component also distinguishes LN/EBA groups from earlier ones at K=16; this component appears to be highly represented in groups from South Asia, the Near East, and the Caucasus. The existence of this component may correspond to the evidence for “dilution” of EHG ancestry in the Yamnaya (SI7), showing them to have evenly split ancestry between the “dark blue” hunter-gatherer and “dark green” component; the analysis of SI9 also suggests an even split between an EHG and a Near Eastern component in the ancestry of the Yamnaya. The “dark green”component seems to have been carried from a Yamnaya-related population to the Corded Ware and other Late Neolithic and Bronze Age populations of central Europe.

A useful topic for future work is to study the relationship of LN/BA populations to contemporary South Asians, Caucasian and Near Eastern populations and to see if this affinity (in contrast to earlier Europeans) may be related to the dispersal of Indo-European languages


According to this paper - Yamnaya may have got their genes from "south Asia" - referring back to the earlier paper I have mentioned above where M417 splits into Z282 and Z93 - where the Z282 went to Europe.

To cut the bullshit and summarize:

European genes have come from Yamnaya, Russia. Yamnaya, Russia may have received South Asian genes as shown by Underhill where M417's son Z 282 went to Europe

Finally I mentioned that there are other Y chromosome genes in India. yes indeed.
Source: http://www.nature.com/articles/srep19157

There is an entity called J2a-M410 which is very widespread in India and includes tribal groups. it appears to have come from the Middle east and is found all over India.

Looking at the image linked below we find that j2a-M410 has a distribution in Northwest India, Iran and well as Russia - just like what we have discussed earlier - i.e M17, Z 93 etc

See image
http://www.nature.com/articles/srep19157/figures/1

In other words there has been a lot of movement between Iran, India and Russia and later Russia and Europe

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Re: Out-of-India - From Theory to Truth: Part 2

Postby Prem » 25 Jun 2016 22:42

http://www.reshafim.org.il/ad/egypt/amarnaletters.htm
A Letter from Tushratta to the King of Egypt
Letters from Biridiya of Megiddo
A Letter from Shuwardata of Keilah
A Letter from Abdu-Heba ( or Adhbudha) of Jerusalem
At the feet of the king, my Lord, seven times and seven times I prostrate myself. What have I done to the king, my Lord? They blame me before the king, my Lord, saying: "Abdu-Heba has rebelled against the king, my Lord."
Letter from Pabi to Akhenaton ( Pabbi is common Khatri Punjabi last name)
You must know that Shipti-Ba'al and Zimrida are conspiring
( Shipti-Bai or Shipti Bal= Bal is one of Jat last name)
Is this Amenhotep might be (R)Aamnahotri ?

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Re: Out-of-India - From Theory to Truth: Part 2

Postby shiv » 26 Jun 2016 08:30

Got this link on email from a 90% lurker BRFite

Cooking the world's oldest known curry
Everyone eats. But what if you were told that 4,000 years ago they ate almost exactly what you ate last night? That re-heating it in the microwave was the only real advantage you had over an average Harappan home cook.

In other words, had you been washed ashore four millennia ago on the banks of the now lost river of Saraswati and hitched a bullock cart ride to Farmana in the Ghaggar valley near modern-day Delhi, here's what you might have eaten - a curry.

For in 2010, when advanced science met archaeology at an excavation site in Farmana - southeast of the largest Harappan city of Rakhigarhi - they made history, and it was edible.

Archaeologists Arunima Kashyap and Steve Webber of Vancouver's Washington State University used the method of starch analysis to trace the world's first-known or "oldest" proto-curry of aubergine, ginger and turmeric from the pot shard of a bulbous handi (pot).

Extracting starch molecules from 50 different surfaces - including pots, stone tools, and the dental enamel of humans and domesticated cows, often fed leftovers - they identified the molecular thumbprints of vegetables, fruits and spices, and studied the effect of heat, salt and sugar on them.

Soon, mangoes and bananas made their mark under the microscope as did dates and gourds. Roasted and boiled, they were each mapped for clues in a lab. Readings of such plant "microfossils" also undercut the dependence on macro-botanical evidence like carbonised seeds and grains in traditional archaeology.

But mostly, they celebrated the building of a new, scientific highway to Harappa. A trapdoor to its kitchens.


Refreshing to read an article from an uncolonized mind - who does not say 'Origins of Harappa are disputed; there was no horse, but there was food"

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Re: Out-of-India - From Theory to Truth: Part 2

Postby shiv » 26 Jun 2016 08:31

From the above - using kookal
Harappan plant use revealed by starch grains from Farmana, India
Our research is providing the first direct evidence for which plants were being used, processed and consumed at the site (Figures 6-9: each image 50µm; Table 1). We have successfully identified starches belonging to barley (Figure 9), millets (Figure 8) and mango from a variety of grinders and pounding stones. Starches of lentils and large and small grained cereals were recovered from the interior surface of storage jars, as for example the starch from Macrotyloma sp. illustrated in Figure 6. Solanum (cf. eggplant), zingiber (cf. ginger) and curcuma (cf. turmeric) (Figure 7) starches were extracted from a cooking pot or handi (a deep narrow-mouthed cooking vessel).

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Re: Out-of-India - From Theory to Truth: Part 2

Postby RajeshA » 26 Jun 2016 19:17

Reading Material

In Quest of the Dates of the Vedas: Comprehensive Study of the Vedic and the Indo-European Flora, Fauna and Climate in Light of the Information ... and Linguistics for the Last 10,000 Years Paperback
Image

Published on Sep 02, 2014
By Premendra Priyadarshi

The dates of the four Vedas, as well as the homeland of the Indo-European-speaking people, have been two unresolved issues in the Indian history. This book uses the robust information recently emerging from archaeo-botanical studies, particularly palinology, as well as that originating from the researches in geology, archaeology, and genetics. The information generated from these scientific studies provides a vivid picture of the last ten thousand years of Europe and Asia. This picture has been matched against the information about the plants, animals, and climate contained in the four Vedic Samhitas, as well as that emerging from the philological studies. The final picture emerges that the Rig-Veda was composed between 8000 BC and 6000 BC, Sama-Veda between 6000 BC and 5500 BC, Yajur-Veda between 5500 BC and 2500 BC, or perhaps 2000 BC, and the Atharva-Veda between 1500BC and 1300 BC. The investigation also reveals that the Indo-European words for "lion" "kesari" "singh" "camel" "ustra" "ostrich" "opium" "lotus" etc. characteristically Indian animals and plants, have existed in the Indo-European vocabulary, although not noticed so far. That exercise fixes the location of the Indo-European homeland in Northwest India at about 10,000-8,000 BC.


Published on Feb 05, 2015
By Premendra Priyadarshi
Vedic Indian Migration to Sumer: DNA evidence

Thus we can see that about 8% of the male Marsh Arab population consists of DNAs of Indian origin. When these Indians went there, they were rich with the wealth of cattle and buffalo. They had the bags of rice seeds and the art of cultivating rice. From the female lineage or the mitochondrial DNA side, we find a larger migration from India to Sumer having taken place. Today it is represented in the Marsh Arab population by the presence of the mtDNA U7, R2 and M (Al-Zaheri 2011:12). One particular sample was found to have mtDNA of the type M33a2a (GenBank accession number: JN540042), which is found in the Uttar Pradesh state of India (ibid). Thus the migrations from India were not male exclusive, but they consisted more of the females. This is understandable, because women play a greater role in paddy cultivation as well as buffalo keeping.

Once the Sumer civilization took off with the help of Indian water-buffaloes and rice cultivation in the South Iraq’s marshes, males of some Semitic tribes arrived to live in the area, and married in this community. They could outnumber the original population. This can be noted today by the 72.8% frequency of Hg J-Page08 in the Marsh Arab population in the male lineage side (Y-chromosomal DNA). The scientific examination reveals that this population (J-Page08) expanded in the region at 4.8 years ago, or about 2,800 BC (Al-Zawahri: Table 2 on page 11). They had arrived there from the northwest (Al-Zaheri 2011:Fig 6). We know from the history that a powerful wave of the Semitic speaking people known as the Akkadian arrived in the region and settled just to the north of the Sumerian marshland establishing an empire about the middle of the third millennium. The Hg J-Page08 male DNA could have been the dominant lineage of the Akkadians. Hence we can say that the Semitic arrival, although male alone, was later than the Indian arrival to the region and it outnumbered the original Sumerians genetically and wiped them out linguistically.


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