From 'Ancient Ancestral South Indians (AASI)' to 'Andamanese Hunter Gatherers (AHG)': Political Pressure on Peer-Reviewed Science Papers?


panuval
 
Edited

As noted by Francesco recently in his posts 17784 https://groups.yahoo.com/neo/groups/Indo-Eurasian_research/conversations/messages/17784 and 17786 https://groups.yahoo.com/neo/groups/Indo-Eurasian_research/conversations/messages/17786, Vasant Shinde, and Niraj Rai, two of the many co-authors of a recent paper published in the journal, Cell https://www.cell.com/cell/fulltext/S0092-8674(19)30967-5?_returnURL=https%3A%2F%2Flinkinghub.elsevier.com%2Fretrieve%2Fpii%2FS0092867419309675%3Fshowall%3Dtrue, deliberately distorted the facts in their own paper in their comments to the media in order to promote a Hindutva viewpoint. Commenting on the views of the above two co-authors as well as a paper by Vagheesh Narasimhan and others published in the journal, Science https://reich.hms.harvard.edu/sites/reich.hms.harvard.edu/files/inline-files/2019_Science_NarasimhanPatterson_CentralSouthAsia.pdf, Tony Joseph, the columnist and author of Early Indians: The Story of Our Ancestors and Where We Came From, said the following in an email interview to Newsclick https://tinyurl.com/y2oy4kd5 dealing with the recent publications dealing the genetics of early South Asians:

“The lesson that media and others need to take from this is that reporting on science needs to be based substantially on the published studies themselves, not the interpretation of the studies by others or even a few of the co-authors after the study has been published in a peer-reviewed journal.

“The published, peer-reviewed study has a kind of durability and robustness that remarks at press conferences do not have.”

As reasons for the distortion by the two researchers, Joseph said the following:
“The Right-wing wants to privilege the Arya-Sanskrit-Vedic culture as the foundational source of Indian civilisation and everything else is to be seen as subservient. It is uncomfortable with the idea that the Harappan civilisation, the largest civilisation of its time by far, precedes the Arya and that we are a multi-source civilisation. It bristles at the concept of ‘unity in diversity’. The one leader, one nation, one culture, one religion, one election... attitude goes well with the idea of one ‘supreme’ culture with a singular foundational source. There is also the issue of not liking the idea of Ary [sic] being migrants, since that would mean you cannot stigmatise Muslims for being migrants— it is another matter that almost all Muslims in India are not migrants.”

While I agree with Joseph’s characterization of the reasons for falsification by the Hindutva-oriented researchers, I would like to note that Joseph has missed a possible devious influence by the Hindutva on the peer-reviewed published papers themselves.

In order to understand this devious influence, we have to go back to the 2018 pre-print https://www.biorxiv.org/content/10.1101/292581v1.fullby Vagheesh M. Narasimhan and others. Let us simply call this Narasimhan preprint or NP. Please note that this preprint points to the published 2019 Science paper as follows "Now published in Science doi: 10.1126/science.aat7487 http://dx.doi.org/10.1126/science.aat7487". Let us call the published Science paper by Narasimhan and others as NSP. Let us call the published Cell article by Shinde and others as SCP.

Consider the abstract/summary of these three papers. There are significant differences in terminology between them regarding ancient hunter gatherers of South Asia, whom Tony Joseph calls ‘First Indians’.

This is what the abstract of NP said: "we develop a model for the formation of present-day South Asians in terms of the temporally and geographically proximate sources of Indus Periphery-related, Steppe, and local South Asian hunter-gatherer-related ancestry." Note the words, "local South Asian hunter-gatherer-related ancestry."

But the abstract of NSP said, "the primary source of ancestry in modern South Asians is a prehistoric genetic gradient between people related to early hunter-gatherers of Iran and Southeast Asia.”

This is what the summary of SCP said, “The individual we sequenced fits as a mixture of people related to ancient Iranians (the largest component) and Southeast Asian hunter-gatherers, a unique profile that matches ancient DNA from 11 genetic outliers from sites in Iran and Turkmenistan in cultural communication with the IVC.”

Between NP and NSP, ‘South Asian hunter-gatherer-related ancestry’ is replaced by ‘hunter-gatherers of… Southeast Asia’. Why? Now consider SCP, which said in its Summary, “The individual we sequenced fits as a mixture of people related to ancient Iranians (the largest component) and Southeast Asian hunter-gatherers…”

If you look further, NP used the designation AASI (Ancient Ancestral South Indians) 27 times. The only time Andaman was mentioned was while defining AASI as given below (ll. 204-205) while describing the admixture modeling:
“Ancient Ancestral South Indian (AASI)-related”: a hypothesized South Asian Hunter-Gatherer lineage related deeply to present-day indigenous Andaman Islanders (19 https://www.biorxiv.org/content/10.1101/292581v1.full#ref-19)

In contrast, NSP used ‘AASI’ 16 times and ‘AHG’ (Andamanese Hunter Gatherers) 16 times. NSP relates AASI and AHG as given below in connection with the admixture modeling.
“AHG, Andamanese hunter-gatherer–related: Represented by present-day indigenous Andaman Islanders (53) who we hypothesize are related to unsampled indigenous South Asians (AASI, Ancient Ancestral South Indians).”


Thus, the earlier primacy of AASI vs. AHG in NP is reversed in NSP. (When one compares NP with NSP, reference 53 seems to be an error for reference 54, the Mallick, et. al., paper of 2016, which is correctly referenced on p. 10 of 15.)

Also, note the description of Figure 4B of NSP:
“Modeling South Asians as a mixture of Central_Steppe_MLBA, AHG (as a proxy for AASI) and Indus_Periphery_West (the individual from the Indus Periphery Cline with the least AASI ancestry).”

Given that AHG is a proxy for AASI, why did NSP choose to use ‘AHG’ instead of simply using ‘AASI’ just as NP did? After all, the admixture graph model in Figure 5 presents the information using AASI and not AHG.

Now consider how SCP referred to AHG. In the explanation of Figure 2 below the figure, we have: “the reconstructed hunter-gatherer population of South Asia (represented by Andamanese Hunter-Gatherers [AHG] who we use as a proxy that we hypothesize is descended deeply in time from the same ancestral population)”. SCP also said on p.4, “Third, both the IVC Cline individuals and the Rakhigarhi individual have admixture from people related to present-day South Asians (ancestry deeply related to Andamanese hunter-gatherers)…” SCP used ‘Andamanese hunter-gatherer’ 5 times and ‘AHG’ 4 times. In Figure 3 on p.5 of SCP, Southeast Asian Hunter-Gatherers were shown to be from (Andaman Islands).

On its part, NSP said on p.10 of 15,
“The graph fits the component of South Asian ancestry with no West Eurasian relatedness (Ancestral Ancient South Asians, AASI) as an Asian lineage that split off around the time that East Asian, Andaman Islander, and Papuan ancestors separated from each other, consistent with the hypothesis that eastern and southern Asian lineages derive from an eastward spread that in a short span gave rise to lineages leading to AASI, East Asians, Andamanese hunter-gatherers, and Papuans (54) (Fig. 5).”

Please note the description, “Ancestral Ancient South Asians, AASI”. We know that AASI stands for Ancient Ancestral South Indians. So the change in word order between ‘Ancient’ and ‘Ancestral’ seems to be an error. The use of ‘South Asians’ instead of ‘South Indians’ could be an error. But it could be intentional if they wanted to convey that the ancient hunter gatherers in South Asia were also ancient ancestral South Indians. This could be due to the statement related to Indus Periphery Cline on p. 4 of 15 of NSP, where we have,
“All 11 outliers had elevated proportions of AHG-related ancestry, and two carried Y chromosome haplogroup H1a1d2, which today is primarily found in southern India.”

In other words, key genetic characteristics of the ancient hunter gatherers of South Asia seem to be primarily found in South India. So, the use of the term, Ancient Ancestral South Indians, by NP seems to be justified. Now let us see what NP has said in connection with its admixture graph in ll. 422-428.

The fitted admixture graph also reveals that the deep ancestry of the indigenous hunter-gather population of India represents an anciently divergent branch of Asian human variation that split off around the same time that East Asian, Onge and Australian aboriginal ancestors separated from each other. This finding is consistent with a model in which essentially all the ancestry of present-day eastern and southern Asians (prior to West Eurasian-related admixture) derives from a single eastward spread, which gave rise in a short span of time to the lineages leading to AASI, East Asians, Onge, and Australians (19).

Thus we have both NP and NSP discussing the same process. If NP could use AASI alone to present the study results, and NSP too used AASI alone in the admixture graph why did NSP introduce the terminology of ‘AHG’ or Andamanese to present the same results? In contrast to both NP and NSP, SCP did not use AASI at all. Given the political leanings of Shinde, one can see a political pressure cline linking the three papers. NSP seems to have met the political pressure half-way. SCP has gone all the way in following the political agenda. But in doing so, presenting the ancient genome of the Indus Valley Civilization individual as “a mixture of people related to ancient Iranians (the largest component) and Southeast Asian hunter-gatherers” is very misleading. This is particularly disturbing given what NSP says regarding Dravidian languages as quoted below.
“Our findings also shed light on the origin of the second-largest language group in South Asia, Dravidian. The strong correlation between ASI ancestry and present-day Dravidian languages suggests that the ASI, which we have shown formed as groups with ancestry typical of the Indus Periphery Cline moved south and east after the decline of the IVC to mix with groups with more AASI ancestry, most likely spoke an early Dravidian language. A possible scenario combining genetic data with archaeology and linguistics is that proto-Dravidian was spread by peoples of the IVC along with the Indus Periphery Cline ancestry component of the ASI. Nongenetic support for an IVC origin of Dravidian languages includes the present-day geographic distribution of these languages (in southern India and southwestern Pakistan) and a suggestion that some symbols on ancient Indus Valley seals de- note Dravidian words or names (63, 64). An alternative possibility is that proto-Dravidian was spread by the half of the ASI’s ancestry that was not from the Indus Periphery Cline and instead derived from the south and the east (peninsular South Asia). The southern scenario is consistent with reconstructions of Proto-Dravidian terms for flora and fauna unique to peninsular India (65, 66).”

Thus, irrespective of whether Dravidian languages were present in Indus Valley or peninsular South Asia, the speakers of Dravidian languages were in South Asia long before the speakers of Indo-European languages (such as Vedic) entered South Asia from the Steppe. This means that the foundational Hindutva claim that the Vedic culture was the sole source of Indian civilization is not valid any more. That is why, there seems to have been a deliberate effort to hide the fact that ancient ancestral South Indians (AASI) formed a major population component in South Asia earlier than those with the Steppe ancestry, who were the Aryan migrants Indologists had talked about for a long time. It should be noted that such Indologists have been attacked by Hindutva activists in the recent decades.

This conclusion is supported by the following statement in the newspaper Organizer in a story dealing with SCP.

“After the Dravidian theorists, few language chauvinists abetted by the Left historians in several Southern states were furthering this theory to de-link the culture, traditions and language of ancient Bharat from the states. They propagated the myth that the 'Aryans' invaded the Dravidians who were the 'original' inhabitants of the area around Harappa and drove them further south. Later when no archaeological or genetic data did not [sic] corroborate this claim, they then proposed the migration myth as per which the ancient Iranians from the West migrated to the Harappan region. Today, they all have to shut shop and try to unite people instead of dividing them based on false and agenda based theories.”

But then, this is not an isolated incident. The Indian government has been trying to put many road blocks https://www.thenewsminute.com/article/keezhadi-excavations-hc-orders-transfer-asi-officer-amarnath-ramakrishna-tn-98413,%20https:/frontline.thehindu.com/arts-and-culture/heritage/article8187801.ece/photo/21/ in the exploration of South Indian history. They have been trying to impose a monochromatic view https://www.deccanherald.com/national/twitter-explodes-over-shahs-one-nation-one-language-761422.html of India. The three papers discussed above reveal the impacts of this continuing political pressure. Fortunately, some media outlets https://thewire.in/the-sciences/rakhigarhi-indus-valley-civilisation-aryan-steppe-migration-vasant-shinde have published articles exposing this politicization of science and truth regarding Aryan migration into South Asia.

David Reich, one of the co-authors of all three papers discussed above, has been deliberately very evasive in his answers to the questions posed by Economic Times https://economictimes.indiatimes.com/news/politics-and-nation/indus-valley-civilisation-is-largest-source-of-ancestry-for-south-asians/articleshow/71042072.cms perhaps in an effort not to antagonize his Indian counterparts. While his answers may have been technically correct, he missed a valuable opportunity to make truth accessible to the public. He could have contributed to the dissemination of truth by clearly answering the questions.


The corresponding authors of NSP, Vagheesh M. Narasimhan, Nick Patterson, Michael Frachetti, Ron Pinhasi, and David Reich, should reveal whatever discussions they had with the representatives of any Indian institutions regarding the anti-South Indian change of replacing ‘AASI’ with ‘AHG’ and ‘Southeast Asian hunter-gatherers’. They owe it to the cause of truth as well as hundreds of millions of South Asians.


Regards,
Palaniappan


Francesco Brighenti
 

Dear Palaniappan,


Let me respectfully dissent from (some parts of) your post archived at


https://groups.yahoo.com/neo/groups/Indo-Eurasian_research/conversations/messages/17791


Your characterization of the classificatory terminology used in the genetic papers we are currently discussing here as a Hindutva-influenced one is out of place.


Let me explain why.


Ancient Ancestral South Indians (AASI) are an unsampled – and, consequently, just hypothesized by Narasimhan et al. – indigenous population of South Asian hunter-gatherers. Their ancestors and those of East Asians, Papuans, and Andamanese separated from one another over forty thousand years ago, namely, during the long journey of modern humans from Africa to Australasia. The geographic area of southern Eurasia in which the AASI lineage split off from (one or more of) the others is not known (could be South Asia itself, or even Southeast Asia with a subsequent backward migration of AASI to South Asia).


Andamanese hunter-gatherers (AHG) are a modern population (indigenous Andaman islanders) selected as a proxy for the AASI, to whom they are related deeply in in time – that’s why Narasimhan et al. always use the expression “AHG-*related*” (not just “AHG”!) to refer to AASI ancestry. The labelling of AASI ancestry as “Southeast Asian” does not imply that AASI were originally a Southeast Asian population, but just that the modern population used by these researchers as a surrogate for them *is* from Southeast Asia (of which the Andaman Islands are part and parcel geographically).


Narasimhan et al. do also contemplate the possibility that the prehistoric, unmixed AASI population of peninsular South Asia spoke some ancient form of Dravidian language. However, it would be hard to argue that Proto-Dravidian dates from the time at which the AASI lineage diverged from the East Asian, Papuan, and Andamanese ones – think, over forty thousand years ago!!!


Keep cool – this team of researchers is not at all trying to hide the fact that AASI were South Indians and to pass them off as “Southeast Asians” instead. That they were possibly Dravidian speakers is, however, an entirely different matter (as there is no genetic “proof” for that).


Best,

Francesco


panuval
 

Dear Francesco,

 

Thank you for your comments. I understand and agree with you regarding your characterization of AASI and AHG(-related) and I am not concerned with the date of proto-Dravidian. My point is different.

 

Just look at the abstract of NSP. It says:

 

"Bysequencing 523 ancient humans, we show that the primary source of ancestry in modern South Asians is a prehistoric genetic gradient between people related to early hunter-gatherers of Iran and Southeast Asia."

But, "Southeast Asia" is never mentioned in the whole paper afterwards in connection with the discussion related to South Asia.


Now look at Figure 5, the admixture graph model shown on p. 10 of 15 of NSP. The admixture graph model has been presented on the basis of AASI alone. For instance, Palliyar are shown to be related to AASI through ASI
, who are related to ‘Iranian-related’ through Indus Periphery West.  But the narrative on the same page says, “Using the DATES software, we estimate an average of 107 ± 11 generations since admixture of the Iranian farmer–related and AHG-related groups in one of these groups, Palliyar.“  Why use ‘AASI’ in the graph model but use ‘AHG-related’ in the narrative?


On p. 3 of 15, when NSP discusses the use of DATES software, it says:

We implemented an algorithm called DATES for estimating the age of the population mixtures (13), which is related to previous methods that translate the average size of ancestry blocks into time since mixture by leveraging precise measurements of meiotic recombination rate in humans (32, 38, 39). DATES has the specific advantage that it is optimized relative to previous methods in being able to work with ancient DNA as well as with single genomes (13). In Box 2, we summarize the findings of these analyses (we use the same headings in Box 2 and the main text to allow cross-referencing), whereas our online data visualizer (1) allows an interactive exploration of the data. 


Please note that they say that they summarize the findings of the DATES analysis in Box 2. But look at what Box 2 on p. 5 of 15 says:

“We identify a distinctive trio of source populations that fits geographically and temporally diverse South Asians since the Bronze Age: a mixture of AASI, an Indus Periphery Cline group with predominantly Iranian farmer–related ancestry, and Central_Steppe_MLBA.”


Thus we see that Box 2 uses ‘AASI’ while the narrative on p.10 of 15 uses ‘AHG-related’ in the discussion on Palliyar. 


Now look at the section called Discussion on p. 11 of 15 of NSP. 

 

"Our analysis reveals that the ancestry of the greater South Asian region in the Holocene was characterized by at least three genetic gradients. Before ~2000 BCE, there was the Indus Periphery Cline consisting of people with different proportions of Iranian farmer– and AASI-related ancestry, which we hypothesize was a characteristic feature of many IVC people."

 

There is no use of ‘AHG-related’ or “Southeast Asia-related” in this discussion. Given this, why bring in ‘Southeast Asia’ or ‘AHG-related’ at all in NSP? After all, NP carried out the entire discussion using ‘AASI’. 

 

While NP uses ‘AASI’ alone, and NSP uses  ‘AASI’ as well as ‘AHG-related’, SCP does not use AASI at all. In contrast to how NSP characterized the three genetic components as seen above, SCP replaces ‘AASI’ with ‘AHG’ in the explanation for Figure 2C on p. 3 of 7 as given below. 

 

“The three components are maximized in Middle-to-Late Bronze Age Steppe pastoralists (Central_Steppe_MLBA), the reconstructed hunter-gatherer population of South Asia (represented by Andamanese Hunter-Gatherers [AHG] who we use as a proxy that we hypothesize is descended deeply in time from the same ancestral population), and Indus_Periphery_West (an individual on the IVC Cline who has one of the lowest proportions of AHG-related ancestry along with the highest-quality data).” 

 

In my opinion, the inconsistent use of ‘AASI’ and ‘AHG-related’ by NSP and the total non-use of ‘AASI’ by SCP shows the origin of the impetus for the use of ‘AHG(-related)’ when it comes to the presentation of results of these studies. I am not saying that Narasimhan, Reich, and others wanted to style NSP this way on their own. I suspect that the Hindutva pressure has forced them to use the mixed terminology they ended up using. After all, as Reich describes in pp. 134-135  of his book, Who We Are and How We Got Here, the designations ‘ASI’ and ‘ANI’ came about due to political considerations.

 

Regards,

Palaniappan


Francesco Brighenti
 

Dear Palaniappan,

 

I understand you criticize the use of the expressions ‘AHG-related’ and ‘related to early Southeast Asian hunter-gatherers’ in place of your top favorite ‘AASI’ because this choice of terms would, in your view, obscure the fact that the AASI were “South Indians” and nothing else.

 

Unfortunately, no ancient DNA sample belonging to the long extinct “pure” AASI has been recovered so far. This is by definition a reconstructed population, not a sampled one. Therefore, I see no problem in characterizing the AASI as ‘AHG-related’ or – which is the same – ‘related to early Southeast Asian hunter-gatherers’ here and there in Narasimhan et al.’s paper. Indeed, such expressions – used as synonyms of ‘AASI’ – merely describe the fact that AASI genome sequences can only be reconstructed based on their relatedness to those of early Southeast Asian hunter-gatherers, of whom modern Andaman islanders (who migrated to the Andaman Islands from Burma, not from India) are considered the direct descendants.

 

Kind regards,

Francesco