La Genetique Scandale — PART 2
by Premendra Priyadarshi
Manipulation of the data and Concoctions
The defective design of research: systemic bias
Bias in modern scientific research and drawing conclusions to fit a narrative is the rule rather than the exception (Mullane and Williams, Eds., Biochemical Pharmacology, Elsevier Journal, 2013; Smith and Noble, British Medical Journal, 2014; Pannuki and Wilkins, Plastic and Reconstructive Surgery 2010).
Narasimhans’ (we will see why not “Narasimhan’s” a little later) paper is a first-class example of how biases can be operative at all the levels and stages of research. If all the manipulations and biases in the article are listed it will perhaps lead to a treatise of 1000 pages, which is not in my intention to do. It will consume at least one year of my time writing such a treatise. Only some very obvious issues, which even a lay reader can understand will be noted below thus.
The admixture analysis and the identification of components
In the admixture analysis presented by them, they have identified some primary components or populations (genetically), which they hypothesise acted as components for the formation of other populations by admixture later in the history. We shall in the first instance see only three of them:
Line 197 (BioRxiv). “Iranian agriculturalist-related”: represented by 8th millennium BCE pastoralists from the Zagros Mountains of Iran (17, 18)”.
Line 201 (ibid). “West Siberian Hunter-Gatherer (West_Siberian_HG)-related”: a newly documented deep source of Eurasian ancestry represented here by three samples”.
Line 204 (ibid). “Ancient Ancestral South Indian (AASI)-related”: a hypothesized South Asian Hunter-Gatherer lineage related deeply to present-day indigenous Andaman Islanders (19)
NOTE: The Narasimhans have used the DNA of the ONGE Tribe of the Andaman Islands to represent this gene pool.
ONGE
The Narasimhans (a handy word in lieu of Narasimhan and colleagues) have chosen to represent the hypothetical Ancient Ancestral South Asians (AASI) by the modern Onge tribe’s genome. The tribe lives in the Andaman Islands today, and are genetically related to the Papua New Guinea tribal peoples from the days of antiquity.
Surprisingly, the Narasimhans’ hypothesise that there were people having an identical genomic constitution as the modern Onge but were living in India until the Iranians and the Steppe people arrived in India. These hypothetical Indians have been labelled as the AASI in the paper. These people supposedly admixed with the Iranian and mid-to-late Bronze Age (BA) Steppe genetic groups to produce the modern Indian population, Narasimhans “conclude”.
In their hypothesis, the admixture of the Onge-genome with the Iranians gave rise to the South Indians (Dravidian) population; and the admixture of this with the Middle-to-late-Bronze Age (MLBA) Steppe population gave rise to the North Indian (Aryan) population, they hypothesise. In other words, it is a resurrection of the Elamite theory of the origin of “Dravidians” in addition to the Aryan Invasion Theory (AIT).
However, the real story cannot be farther from the truth. Onge people could have been of the same genetic composition as the Indians about 70,000 to 50,000 years back, but not today, not even 10,000 years before today.
These people (Onge) are the remnants of the people who migrated to these Islands and also to Southeast Asia about 70,000 to 50,000 years back. Some could have probably stayed back in India. They had arrived into Andaman (ancestors of the Onge and Jorwa), and have migrated further eastward towards Papua New Guinea and Australia. Thus, the Onge population got separated from the rest of the humanity (and definitely mainland Indians) about 50,000 to 70,000 years ago, noted Thangaraj et al (2005) in their genetic study: “this was the same time when the Australians (and the Papuans) separated from the rest of the humanity.”
NOTE: It is the same Thangaraj who is now a co-author in the Narasimhans paper doing a circus somersault.
In fact, they had not stopped at Australia but had even reached South America, whose descendants are living there till today. (Skoglund et al Nature 524:104–108, 2015; David Reich was one of the authors of this article). They noted that these (Onge, Papuan, Australian) form the Australasian family.
Thus, these (Onge) must be considered only much more remotely (in the past) connected to the Ancient Ancestral South Asians, than are the European Cro-Magnons, Siberians, Iranians and the Central Asians who branched off from the main basal Eurasian trunk much later in time than the Onge did.
It is useful here to recollect what Thangaraj wrote about the Onge: “Our data indicate that the two ancient maternal lineages, M31 and M32 in the Onge and the Great Andamanese, have evolved in the Andaman Islands independently from other South and Southeast Asian populations.
These lineages have been shown to be isolated since the initial penetration of the northern coastal areas of the Indian Ocean by anatomically modern humans, in their out-of-Africa migration 50 to 70 thousand years ago.” (Thangaraj et al, 2005, Reconstructing the Origin of Andaman Islanders, Science, 308 (5724): 996)
Thangaraj also noted that over that period of time the genetic composition of the populations of the Andaman-Onge and Indian-Mainland population drifted from each other due to changes taking place in the two independently. They note: “Analysis of the complete mtDNA sequences shows that none of the coding region mutations defining these two haplogroups overlaps with the known Indian or East Asian mtDNA haplogroups. In our survey of 6500 mtDNA sequences from mainland India, none of the M lineages carried the coding region mutations specific to M31 and M32 (6).” (Thangaraj 2005). Thus, we can see that genetically the Onge had deviated / separated and have evolved independently from mainland India over the last 50,000 years, or more, of the separation.
Thus, considering Onge as the Indian population at the onset of Neolithic discredits the entire work, and has completely vitiated all the conclusions.
Instead of identifying Onge as a (pure) single component, somehow their admixture analysis seems to have found that it is an admixture with the Iranian DNA. This error occurred because the authors failed to recognise that the Onge and the Iranians both had split from the mainland Indians, although in vastly different eras, tens of thousands of years apart.
Obviously, given the very ancient commonality between the three populations (Onge, mainland Indian and Iranian) there must be some elements common in the three. Of course, there would be some portions which would be distinct as well in the three populations due to the separation and consequent independent evolution.
This failure to appreciate some commonality (due to the common origins) between Indian and Iranian DNAs resulted in considering the Iranian farmers as an “unmixed” pure component, while the Onge population removed by more than thousands of miles of deep sea is laughably considered an admixed population.
It was also compounded by the false and erroneous prejudice that nobody could ever have gone out of India (OIT). In an effort at negating the Indian components in the Iranian Agriculturists, the authors “tweaked” (to put it mildly) the parameters in such way so that the Iranian Agriculturists falsely appear to made up of a single component, coloured teal (light blue) in the admixture analysis.
Such questionable distortions, in the “calibration,” have vitiated the entirety of the results in such a way that the mono-component genome of the Onge (Andamanese) started showing up as if it was made of two components (admixed). One of them was blue (Iranian Agriculturists) as depicted in the admixture “histogram” in the above figure.
How it happened can be seen in the figure below:
Iranian (Jagros Neolithic): Ganj Dareh
The Ganj Dareh has been postulated as one of the principal components in the Narasimhan study. However, it has clear ancestry from Northwest Indian sub-continent, where Pakistan is located today. Narasimhans’ own figures (and data) themselves show that the Ganj Dareh is only a subset of the larger set which is Onge, Mala and other Indian samples.
Unfortunately for the Narasimhans, the Ganj Dareh (Iranian Neolithic) DNA had been studied by another group of researchers whose work was published in Nature (which appears to be not as biased as the journal widely known as the Science magazine). They found that:
“The mitochondrion of GD13a (91.74X) was assigned to haplogroup X, most likely to the sub-haplogroup X2, which has been associated with an early expansion from the Near East and has been found in early Neolithic samples from Anatolia, Hungary and Germany.” (Llorente 2016)
“GD13a did not cluster with any other early Neolithic individual from Eurasia in any of the analyses.” (Llorente 2016)
Interpretation: We need to remember that no South Asian Neolithic DNA has been reported so far. Thus, if GD13a matched none, possibly only one which remains to be tried is the South Asian Neolithic DNA.
“We further investigated the relationship between GD13a and Caucasus Hunter-Gatherers using D-statistics to test whether they formed a clade to the exclusion of other ancient and modern samples (Table S4). A large number of Western Eurasian samples (both modern and ancient) showed significant excess genetic affinity to the Caucasus Hunter-Gatherers, whilst none did with GD13a. Overall, these results point to GD13a having little direct genetic input into later European populations compared to its northern neighbours.” (Llorente 2016)
Interpretation: Thus the oldest Iranian Agriculturists of the Ganj Dareh had not directly migrated to Europe, although their mitochondrial DNA X2 certainly contributed to the modern European population. Other studies have shown (see below) that the Iranian Neolithic DNAs had migrated to Levant and Anatolia, and the Caucasus as well as the Steppe. Clearly, the Ganj Dareh DNAs were not the gross representative of the Iranian Neolithic, but they represent a segment which was very small and did not make much impact on later Europe, Caucasus or the Steppe. It might have represented just a small number of the emigrants from a single village in Balochistan or other parts of northwest South Asia (pre-modern India), and might have represented only a tiny fraction of genetic variation which South Asia had at that time. On the other hand, the people reaching the other locations in Zagros (Iran) at Neolithic might have originated from other villages of present-day Pakistan/ Afghanistan resulting in differences (diversity) in genetic composition within the Zagros Neolithic populations.
“The individual analysed here was part of burial 13, which contained three individuals, and was recovered in level C in 1971 from the floor of a brick-walled structure. The individual sampled, 13A (referred to as GD13a throughout the text), was a 30–50-year-old female; the other individuals in the burial unit were a second adult (13B) and an adolescent (13). The site has been directly dated to 9650–9950 cal BP, and shows intense occupation over two to three centuries. The economy of the population was that of pastoralists with an emphasis on goat herding. Archaeobotanical evidence is limited but the evidence present is for two-row barley with no evidence for wheat, rye or other domesticates. This implies that the overall economy was at a much earlier stage in the development of cereal agriculture than that found in the Levant, Anatolia and Northern Mesopotamian basin.” (Llorente 2016)
Interpretation: This information refutes the claim by the Narasimhans that the Mehrgarh farming culture had been borrowed from Anatolia (Turkey) through Iran (Ganj Dareh). The date cited above gives a date of 7,850 BC (mean). It may be noted that the Mehrgarh oldest layer has a date of 8,707 BC (mean).
While the Ganj Dareh Iranian people had only two-row barley (see above) at 7850 BC, the Mehrgarh had six-row barley at 8700 BC, which is an advanced stage of agricultural development and domestication of barley (Upinder Singh 120; Jarrige 2008).
Jarrige wrote, citing Lorenzo Costantini:
“Lorenzo Costantini has shown that the plant assemblage of Period I is dominated by naked six-row barley which accounts for more than 90% of the so far recorded seeds and imprints. He has also pointed out the sphaerococcoid form of the naked-barley grains with a short compact spike with shortened internodes and small rounded seeds.
According to him, such characteristics in the aceramic Neolithic levels can be ascribed to probably cultivated but perhaps not fully domesticated plants. Domestic hulled six-row barley (H. vulgare, subsp. vulgare) and wild and domestic hulled two-row barley (H. vulgare subsp. spontaneum and H. vulgare subsp. distichum) have also been recorded, but in much smaller quantities. According to Zohary quoted by R.H. Meadow, the distribution of wild barley extends today to the head of the Bolan Pass. It is therefore likely that local wild barleys could have been brought under cultivation in the Mehrgarh area. Costantini has also identified a small amount of domestic einkorn (hulled: Triticum monococcum), domestic emmer (hulled: T. turgidum subsp. dicoccum) and a free-threshing form which can be referred to as Triticum durum (Fig. 10).” (Jarrige 2006)
Interpretation: Thus, these people of Iran had arrived here about 1000 years after the Mehrgarh culture had taken off. The Ganj Dareh site had been occupied for only a short period of 100 to 300 years (mean 200 years). On the other hand, the Mehrgarh shows a continuous occupation for a long and continuous period till recent times. It may be noted that the domestication of the goat is not possible to take place in 200 or 300 years and about a thousand years is required for the features of domestication to start appearing on the skeletons of the animals. Clearly, the people of Ganj Dareh were not local, and had arrived from somewhere else.
“ADMIXTURE and outgroup f3 statistics identified Caucasus Hunter-Gatherers of Western Georgia, just north of the Zagros mountains, as the group genetically most similar to GD13a (Fig. 1B,C), whilst PCA also revealed some affinity with modern Central South Asian populations such as Balochi, Makrani and Brahui (Fig. 1A and Fig. S4).” (Llorente 2016)
Interpretation: It is possible to interpret it as the Ganj Dareh coming from a region within the locations of Brahui, Baluchistan and Makaran of South Asia, now in Pakistan. Mehrgarh was in modern-day Baluchistan.
“Also genetically close to GD13a were ancient samples from Steppe populations (Yamanya & Afanasievo) that were part of one or more Bronze age migrations into Europe, as well as early Bronze age cultures in that continent (Corded Ware) in line with previous relationships observed for the Caucasus Hunter-Gatherers.”
Interpretation: Yamnaya and Afanasievo of steppe/ Central Asia were much later than Ganj Dareh (Iran). The resemblance could be due to either the Iranian early farmers migrating into the Steppe. But these people could have developed from the migrations from the northwest India/ Afghanistan/ Pamir region. The Pamir is a likely source for R1b which migrated by northern Iranian/ Turkmenistan wet corridor to the south of Caspian and then from there to Armenia, Anatolia and then the Southern, Western and Central Europe. Yamnaya and Afanasievo samples belong to R1b Y-DNA. See figures below.
Now let us see what Llorente had to say further on Ganj Dareh:
“We further investigated the relationship between GD13a and Caucasus Hunter-Gatherers using D-statistics to test whether they formed a clade to the exclusion of other ancient and modern samples (Table S4). A large number of Western Eurasian samples (both modern and ancient) showed significant excess genetic affinity to the Caucasus Hunter-Gatherers, whilst none did with GD13a. Overall, these results point to GD13a having little direct genetic input into later European populations compared to its northern neighbours.” (Llorente 2016)
Interpretation: Later Europeans are products of another wave of migration namely R1b which came later in the Bronze Age.
“Thus, GD13a is the descendant of a group that had a relatively stable demography and did not suffer the bottlenecks that affected more northern populations.” (Llorente 2016)
Interpretation: This line points to India as the origin for the present day Eurasians.
What about other characters of the Ganj Dareh lady? Llorente noted the skin colour of the Ganj Dareh lady:
“She lacked the derived variant (rs16891982) of the SLC45A2 gene associated with light skin pigmentation but likely had at least one copy of the derived SLC24A5 allele (rs1426654) associated with the same trait. The derived SLC24A5 variant has been found in both Neolithic farmer and Caucasus Hunter-Gatherer groups suggesting that it was already present at an appreciable frequency before these populations diverged. Finally, she did not have the most common European variant of the LCT gene (rs4988235) associated with the ability to digest raw milk, consistent with the later emergence of this adaptation.” (Llorente 2016).
Clearly, she had the light skin colour gene SLC24A5 allele which produces light skin colour in the Europeans and the Indians (Basu Mallik et al 2013). This gene was not found in the Europeans until late the Bronze Age. It was not present in the La Branda human of 5000 BC. However, it was found present in many European people between 3000 BC and 1000 BC (Allentoft). This means the Ganj Dareh were not ancestral to the early Neolithic people of the north of Black Sea who entered East Europe replacing the hunter-gatherers at about 5000 BC.
I have earlier demonstrated that the light skin colour gene SLC24A5 originated in South India long back, and it migrated to other places including even Ethiopia from India.
Another researcher in the field, Broushaki, in 2016 noted that the Iranian Neolithic people from Wezmeh Cave were related to the Pakistani and Afghan people, particularly the Zoroastrians of Iranian origin now living in India. “These people are estimated to have separated from Early Neolithic farmers in Anatolia some 46–77,000 years ago and show affinities to modern day Pakistani and Afghan populations, but particularly to Iranian Zoroastrians.” Clearly, the Zagros (Iran) farmers had not arrived from Anatolian farmer community of the Anatolia Neolithic. In fact, they are deeply related to the Indian population.
The Western Siberian Hunter-Gatherers (HG)
Narasimhans have selected the following samples as representing the West Siberian DNA:
- Sosnoviy-Ostrov, western Siberia, Russia (n=1); Tomsk10 (I5766): Date of 4230–3983 cal BCE (5261±33 BP, OxA-33486, d15N=+12.8 possible marine influence). Genetically female.
- Tyumen Oblast, western Siberia, Russia (n=2) Tyumen1, Kurgan 1 (I1958): Date of 4723–4558 cal BCE (5805±25 BP, PSUAMS-2359), Genetically female
- Tyumen50, Kurgan 6 (I1960): Date of 6361–6071 cal BCE [6335–6071 cal BCE (7330±40 BP, Poz-82198), 6361–6086 cal BCE (7355±40 BP, OxA-33489, d15N=+15.3 permil possible marine influence)]. Genetically female.
These places Sosnoviy-Ostrov and Tyumen Oblast by foot are about 3400 km to the north of Kabul. They had been coded as yellow colour (AASI, Indian, Onge) component, about one third quantitatively in the admixture analysis.
It appears that to mislead people, this fact has been blatantly denied, not by changing the colour of the component, but by considering it an entirely different component, although it appears the same as the Indian.
Apart from this de Barros Damgard et al have provided another set of admixture “histograms” for the admixture analysis of the same populations, with locations marked. This is more honest, correct and appears to be not tampered with.
If rearranged, this picture gives the following:
This figure indicates that the Indian cline should be defined as East to South to Northwest in a folded shape or V-shape. There is a gradual change in proportions of the golden, pink and teal (bluish-green) colours. Such arrangement indicates natural settlements with genetic changes produced not by migration but by the Brownian Movements (natural drift) of the genes.
If any arrival takes place, there must be a breach in the cline in the same way that Broushaki got one, between Zagros and Anatolia during the Neolithic.
The further summation of the components indicates that the Steppe may have originated from northwest India:
We know from other studies of a lot of the ancient samples of Y-DNA H1 lineage, which is typically Indian, and most probably of South Indian origin later expanding to North India, have been found from Eneolithic to Bronze Age periods from locations in Anatolia, Middle East (e.g. Namazga), and North of Mongolia (Lake Baikal region, Shamanka). Clearly, Indians had been migrating to wider regions of Asia much before the Steppe culture took off during the Bronze Age period. (See Supplementary matter Excel Table aar7711_Table 14, of de Barros Damgaard, Science 2018).
Thus we can conclude as this picture:
The H1 had a sibling H2 which has been found from the Neolithic samples of Levant, Anatolia, and Sardinia. It has also been found from West Lake Baikal Shamanka region from the Eneolithic period (sample number DA339 in de Barros Damgaard 2018, see table). H3 is another branch which is found in the Romany.
The early branch H0 which had split the earliest from the main trunk of H is found in India alone.
