What are ANI and ASI? What are the European and Indian R1a branches? Some explanations to the findings of David Reich et al 2009 and later works

by P. Priyadarshi



It has been settled so many times by several repeated studies that the modern man came out of Africa from the horn of Africa (Djibouti) crossing Bab-el-Mandeb Strait then through coastal Arabia to Sind-Gujarat region of India (Quintana-Murci 1999; Oppenheimer 2003; Maccaulay 2005; Mellars 2006; Thangaraj 2005; Field 2007; Armitage 2011; Mele 2012). And it has also been conclusively decided that the human migration out of Africa took place only once and not the second time again.


The most sophisticated method of study for the purpose of finding out the Out of Africa route was adopted by the Genographic Project which was funded by IBM, the computer giant. The method was so refined that it could map each step of a thousand mile journey. This method was the most accurate also. It produced the following map of the routes of human migration.

Geno Project Human Migration Map_print

Source: Genographic Project web site. http://www-03.ibm.com/press/us/en/photo/35881.wss 

also, https://www-03.ibm.com/press/us/en/pressrelease/35877.wss

Their press release said, “Over the past six years, we’ve had the opportunity to gather and analyze genetic data around the world at a scale and level of detail that has never been done before.  When we started, our goal was to bring science expeditions into the modern era to further a deeper understanding of human roots and diversity. With evidence that the genetic diversity in southern India is closer to Africa than that of Europe, this suggests that other fields of research such as archaeology and anthropology should look for additional evidence on the migration route of early humans to further explore this theory.”


However this good advice was ignored by later workers, however, Priyadarshi (2014) tried to look for additional evidence in archaeology and anthropology to correlate with this route, and he achieved remarkable success. The results of the Genographic team’s study were largely ignored by the Eurocentic dominated academic community which is dominant.


The workers of the Genographic Project also said, “The new analytical method looks at recombinations of DNA chromosomes over time, which is one determinant of how new gene sequences are created in subsequent generations. Imagine a recombining chromosome as a deck of cards. When a pair of chromosomes is shuffled together, it creates combinations of DNA. This recombination process occurs through the generations.”


“Recombination contributes to genome diversity in 99% of the human genome. However, many believed it was impossible to map the recombinational history of DNA due to the complex, overlapping patterns created in every generation. Now, by applying detailed computational methods and powerful algorithms, scientists can provide new evidence on the size and history of ancient populations.” (source web site, link provided below the figure above).


An article was published on the basis of this study which said in its Abstract, “We also observe that the patterns of recombinational diversity of these populations correlate with distance out of Africa if that distance is measured along a path crossing South Arabia. No such correlation is found through a Sinai route, suggesting that anatomically modern humans first left Africa through the Bab-el-Mandeb strait rather than through present Egypt.” (Mele et al 2012:Abstract).


The article further noted, in the context of the other method based on SNPs, “And the two approaches may reflect processes taking place in different time frames with the recombination-based analysis being more sensitive to more recent events.” (Mele 2012:28) Thus the migrations taking place during the last 10,000 years, particularly the Indo-European migrations can be best described by the migration routes described by the Genographic Project’s study. Thus it is settled that there was only one route out of Africa and people using the Arabian coast reached India to expand further.


However an obsession to stick to his untenable position of the Egyptian route to Europe, West Asia and Central Asia, kept Reich and his group continuously making mistakes after mistakes in analysing the data emerging from all the later studies.


Thus in light of the above discussion, if we examine the data of Reich (2009), it gives entirely different inferences. Metspalu (2004) and Sahoo (2006) had demonstrated that there is a paucity of mtDNA and Y chromosome lineages in the Indian gene pool that have been assigned a Central Asian origin (Metspalu et al. 2004; Sahoo et al. 2006). This in other words means there was no measurable, if at all, arrival from Central Asia to India. Metspalu (2004) also noted that about 10% of mtDNAs (haplogroup M) of Iran were of Indian origin.


Sahoo et al (2006:847) demonstrated that although the DNA haplogroups of South Asian (India-Pakistan) origin are found in West Asia, other common lineages of West Asia are not found at all in India-Pakistan; and therefore they concluded that no migration from Middle East had taken place to Indian subcontinent, although migrations from India to Middle East had taken place.


Sahoo et al had actually written the following words: “The perennial concept of people, language, and agriculture arriving to India together through the northwest corridor does not hold up to close scrutiny. Recent claims for a linkage of haplogroups J2, L, R1a, and R2 with a contemporaneous origin for the majority of the Indian castes’ paternal lineages from outside the subcontinent are rejected, although our findings do support a local origin of haplogroups F* and H.” (p. 847). They also rule out arrivals from Southwest Asia because West Asian haplogroups (like Y-Hg G) are not found in India.


Kivisild’s findings (2003:322, column 2) too had shown that humans could not have arrived from West Asia into India because of lack of West Asian Y-hgs E, G, I, J* and J2f in India. Kivisild et al wrote, “When compared with European and Middle Eastern populations (Semino et al. 2000), Indians (i) share with them clades J2 and M173 derived sister groups R1b and R1a, the latter of which is particularly frequent in India; and (ii) lack or show a marginal frequency of clades E, G, I, J*, and J2f.”


The Root Cause of Continuing Confusion


There were mtDNAs as well as Y-DNAs which were present in both–India and Iran on the one hand and in Europe on the other hand. This led the Eurocentric academicia to proclaim that these were Western European DNAs. These included for example, Y-DNA J2, R1a, R1b etc and mtDNA H, U, T etc. This assumption was used as evidence favouring Indo-Iranian arrivals from Europe. The sharing of ANI (Ancestral North Indian) genes by European, West Asian and Central Asians as shown by Reich (2009) was considered as proof of about 50% of north Indians having arrived from Central Asia, West Asia and Europe (Tamang, Singh and Thangaraj 2012; Metspalu 2011). However the other possibility that the Ancient North Indians (ANI) people might have migrated to Europe, West Asia and Central Asia was not given any heed. The Aryan Invasion Theory was working hard in these minds.



Mist Cleared by Ancient DNA


Ancient DNA or aDNA are DNAs recovered from the skeletons recovered from part. Recently the technology has advanced much and now we know the things much better about the humans of the past. The ancient DNA (aDNA) studies showed that the population of Europe had been replaced by people arriving there from East Asia, Caucasus, West Asia and Iran during the Holocene. The original hunter-gatherer population of Europe became almost extinct except in some warmer regions like Iberian Peninsula (a fraction of people of Spain). People arrived in Europe starting about 7000 BC, but mainly after 5500 BC. The most of the modern population of Europe came there from Asia between 5000 and 4000 BC. However, many continued to arrive even up to 1000 BC. This is in nutshell the peopling of modern Europe as derived from ancient DNA studies (Olalde 2014; Haak 2015; Allentoft 2015; Der Sarkissian et al, 2013; Fu et al, 2016).


Thus, today’s European or Western Eurasian haplogroups are not European in origin but are in fact Asian in origin; and the European or Western European gene or haplogroup is a misnomer and now needs to be discarded.


The R1a Controversy


The current debate is over the place of origin of the R1a or R1a1 (named differently in different articles). Underhill (2010) had noted that, “Importantly, the virtual absence of M458 chromosomes outside Europe speaks against substantial patrilineal gene flow from East Europe to Asia, including to India, at least since the mid-Holocene.” (Underhill 2010:Abstract, last line). The R1a-M458 is the European branch of R1a1. Had people come from East Europe like Ukraine etc moved to India this branch must have come to India. But it did not happen. It is not found in India today.


The fuss created by some people about two different branches of R1a Y-DNA—one Indian and one European–can now be sorted out by means of the ancient DNAs, and there is no room for speculation. The Indian branch of R1a, i.e. R1a-Z93 is exclusive of India, Pakistan and Afghanistan. It originated in India and migrated through the Pamir route during the Bronze Age to Altai region and even to Sintashta (Ukraine), the Cradle of Western Indo-European culture.


Brief story of R1a Controversy


The Y-chromosomal DNA haplogroup R1a was identified by a marker M17. This Y-DNA R1a or M17 is widespread in the living population of Eurasia—from India to Europe through Central Asia. This finding prompted many authors to link it with the Indo-European migration. Wells (2001) claimed that the humans made their first settlement in Central Asia, and that the M17 was born in Central Asia from where it reached India with the Aryan invaders in about 1500 BC. “This pattern of high diversity is consistent with an early settlement of Central Asia by anatomically modern humans, perhaps 40,000–50,000 years ago (see below), followed by subsequent migrations into Europe, America, and India,” (Wells 2001: 10247)


By 2006, another identifying mutation M198 was identified by the scientists for the same DNA, and the particular DNA was given the new name R1a1-M198 (or, R1a1-M17). This is now its preferred name. Regueiro (2006) claimed that the DNA R1a1-M198 had originated in the Kurgan culture of the steppe from where it migrated into India. He noted, “This finding supports the inferred migration of the Indo-Iranians during the period 3,000 to 1,000 B.C. as proposed by Mallory” (Regueiro 2006:140).


However such views were based on the Aryan Invasion Theory; and there was no supporting evidence regarding the direction of migration. Later Evidence favouring Indian origin of R1a1 Later on, voluminous DNA evidence emerged which proved that the place of origin of this DNA was India and that it had later migrated into Central Asia, from there to Volga-Ural region and from there to East and then Central Europe. Yet, ironically, in general many authors till date ignored the recent evidence and continued to say that this DNA originated in Ukraine from where migrated to Central Asia, India and Europe. Stephen Oppenheimer too holds this view privately as communicated to me in a meeting held at Lalit Hotel in Delhi.


Several researchers pointed out on the basis of the further analysis that this male lineage of DNA known as R1a1 had not arrived from outside but was indigenous to India (Sahoo 2006; Sengupta 2006; Sharma 2009). These researches also noted the formidable presence of this DNA (R1a1) in the Dravidian speaking South Indians as well as the Austro-Asiatic speaking tribal groups. In fact this DNA had migrated to Southeast Asia also from where it even reached Madagascar.


Underhill (2010) further examined this DNA and found that the oldest haplotypes of the DNA was present in India and it expanded from India (Indus Valley region) to Central Asia and then to Europe as well as Mongolia (Underhill 2010:Fig.1). He was able to identify two branches within this lineage with the help of two markers. One branch identified by the marker M434 was distributed in West Asia and it also migrated into Arabia. The other branch was identified by the marker M458 and it was restricted to Europe with a particularly high concentration in East Europe like Ukraine.


However not a single person belonging to this branch could be found in India or Iran. Thus Underhill ruled out any migration from Ukraine or from the adjoining steppe to India or to any other part of Asia. “Importantly, the virtual absence of M458 chromosomes outside Europe speaks against substantial patrilineal gene flow from East Europe to Asia, including to India, at least since the mid-Holocene.” (Underhill 2010:Abstract)


Pamjav (2012) was able to find finer details about the branches of the R1a1 lineage. He noted that the M458, earlier identified by Underhill, and another branch Z280 were found in Europe, whereas the branch Z93 had split from the main trunk in India. Thus it became clear that the main trunk M198, gave birth to branch Z93 in India from where it spread to Uzbekistan and Mongolia, as well as to Southeast Asia (Pamjav 2012:2). Some members of this Indian branch Z93 also reached up to Hungary independently of any Roma migration (ibid: 3). This means Indians certainly migrated to Mongolia, Central Asia and Hungary after the birth of this branch. And of course they could have migrated before the birth of this lineage in the earlier eras.

R1a-Z93-Asia Eupedia

Fig. Source Eupedia. The distribution of Indian R1a-Z93 indicating its origin in India nad migration through the Pamir to Tarim Basin and Altai, and from there to the steppe.

The European branches of R1a1 namely M458 and Z280 originated while the main trunk was passing through the Caucasus region and the steppe (Pamjav 2012:Abstract). Then the whole group of people moved forward into Europe through the North Black Sea region. Hence we get M458 and also Z280 in the steppe, East Europe and Central Europe but not in India or Iran. “Inner and Central Asia seem to be the overlap zones for the R1a1-Z280 and R1a1-Z93 chromosomes as both forms were observed at low frequencies.” (ibid:3)


This is because the Indian branch Z93 also migrated into Central Asia along with its parent main trunk M198. But the European branches found in Central Asia and the steppe never came to India. It is big evidence which clarifies the direction of human movement. Hence the Indian branch can be found today in Mongolia, Central Asia and even in Hungary today. But the European branches (M458 and Z280) cannot be found in India. This finding irrefutably fixes the direction of migration as to be from India to Europe, and leaves no room to any further argument in the matter.


Underhill (2015) was made pariah for his bold statement made in Underhill (2010). Yet even under great pressure he never accepted the European or steppe origin of the R1a trunk. He further worked on this lineage and found that the R1a1 has several branches which can be grouped into two. One set of branches are found in India and Central Asia, where as the other set of branches are found in Europe.


Of the European samples of R1a, 96% belonged to Z282, and 98.4% of Indian and Central Asian lineages belonged to the lineage Z93. Underhill (2015) found that one branch M558 originated in Volga-Ural area and migrated with the group further west into East Europe. The branch M458 broke off after that. Only after these, the branches M282 and M284 originated.


The Indian branch Z93 is quite common today in South Siberia, Altai region of Russia, Kyrgyzstan and Iran. The further branches of Z93 lineage are 1. Z2124 found in Pashtun Afghanistan, Caucasus and Iran; 2. M750 in India, Pakistan, Afghanistan and Himalayas; 3. M560 in Burushaski, Hazara, and Iranian Azeri (Underhill 2015:11).


Underhill in his latest work proposed the place of origin of R1a somewhere “near Iran” (2015:11-12). But instead of saying “near Iran”, saying Indian sub-continent would have been more accurate.  His conclusion does not take into account of the R1a lineages present in the Indian tribes and Dravidian speakers. They were not included by Underhill (2015) in his study. His study also did not include the study of R1a present in several eastern regions of India like Bihar, UP, as well as R1a present in Myanmar, Thailand, and Indonesia etc.


The Y-DNAs R1 (M173) and R* (M207) are found in large numbers in Bali (Indonesia) today, and they have migrated there from India (Karafet 2005:Table 1). In fact at least 12% of Balinese male lineages were found to be of Indian origins in this study. These R1 DNAs are ancestral to R1a1. Kusuma (2015) found that R1a lineage has reached Madagascar (Malagasy) also when people of Indonesia migrated to this island. Such findings only prove that R1a1 originated in India and not in Iran.


More truth is revealed by the recovery of the R1a1 samples from the archaeological samples of human remains. One R1a1a has been found from 5100 BC Spain at Els Trocs site (Haak 2015). This is a descendant of R1a1a. This could have migrated there with the goat-pastoralist migration which took place from India to Southwest Europe through Ganj Dareh (Iran) about that time. One R1a1 has been found from Oleni Ostrov (Northwest Russia) dated 6,400 BC (Mesolithic Culture; Haak 2015). Earlier than these two findings, there has been no R1a1 lineage in Europe.


Also, five samples of India branch that is R1a-Z93 have been found from the Bronze Age Sintashta (Ukraine) about 2500 BC (Mathieson 2015: page 4). Sintashta is currently being considered the cradle and source of the Indo-European language and Culture of Europe. It has been repeated by these authors that Indo-Aryans and Iranians came to India and Iran from Sintashta. However the presence of Indian DNA there clearly indicated whether Indo-Europeans came to India from Sintashta, or went from India to Sintashta.


Apart from these two examples, the R1a1 did not migrate to Europe in large numbers during the Neolithic period. Its general migration from India and Iran to Central Asia and Europe took place mainly during the Copper, Bronze and the Iron Ages, which was also the time of rise and fall of the Indus Valley Civilization. This shows that this lineage got established in the Indus Valley just before its rise in about fifth millennium BC, and it also proves that the Bronze Age Indus Valley Civilization was Indo-European civilization.


The Tarim Basin mummies recovered from Xinjiang in Central Asia had all males in the R1a1 (M198A) lineage (Li 2010), which is Indian. The date was late Bronze Age to Iron Age. Since the lineage was not present in Europe in such large frequency at that time and before this time, its arrival could have been only from India or Iran. The high frequency may be because of the founder effect. Other evidence also shows migration during that period from India/ Iran. Li (2015) further clarified that the Tarim Basin mummies carried Indian maternal DNAs in good frequency.


Recent finding of ancient DNA from the Indo-European Maikop culture dating 3700 BC in North Caucasus further adds weight to Indian origin of Indo-European. Skolov (2016) found that several of the ancient mtDNAs recovered from Maikop belonged to the Indian M52 type. Thus proving that the Maikop people had arrived from India, and they had included female migrants too.


Understanding Reich et al 2009 in light of the foregoing


David Reich’s problem was that he failed to reconcile himself with the fact that there was no other route of Out of Africa than the coastal Arabian route to India, and thereafter expansion and migrations took off from here. He continued to harbour the concept of the second route to Europe and Central Asia through Egypt and Sinai to West Asia and then beyond. This created distortions in all the interpretations done by himself or the group of his follower scholars. In light of the ancient DNA findings, and also some robust extant DNA studies, it is desirable that ‘Reich et al 2009’ should be re-explained in more simple English once again so that people may wash their prejudiced views.


Reich et al (2009) nowhere said that there was any flow of west Eurasian (European) gene into South Asia. To quote their own words, “These results do not mean that the Indian groups descend from mixtures of European and Austro-Asiatic speakers, but only that they derive from at least two different groups that are (distantly) related to CEU and Santhal.” (p. 4 pdf, col 1).


Relatedness does not at all imply gene flow from CEU (Europe) to India, however it means a common ancestor for both north ancestral Indians and CEU. This common ancestor had existed after split from the African main trunk, and after the Ancestral South Indians too had been split. Reich et al depict this situation by means of a figure (Fig. 4 of Reich et al). The figure of migration which Reich et al produced can be seen at the link below:

( http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2842210/figure/F4/ or,


or, see Fig 4, page 4 of pdf of the article.)


Figures for family tree can be constructed from the text itself actually. Reich et al write, “the tree (YRI,((CEU,ANI),(ASI, Onge))) provides an excellent fit to the data”. This gives us a family tree for five populations, viz. 1. YRI (West African), 2. CEU (Modern Europeans), 3. ANI (Ancestral North Indians), 4. ASI (Ancestral South Indians) and 5. Onge (a Modern Andamanese tribe)—if drawn graphically would be like this:

Reich 1

The top inset from Stephen Oppenheimer’s The Journey of Mankind, Bradshaw Foundation has been added as a ready-reminder to African-Eurasian split and relationship. Source: http://www.bradshawfoundation.com/journey/



This is clarified further in the text of Reich et al: “the fact that different Indian groups have inherited different proportions of ancestry from the ‘Ancestral North Indians’ (ANI) who are related to western Eurasians, and the ‘Ancestral South Indians’ (ASI).”


Here we note that, in spite of the fact that ANI were related to Western Eurasians (Europeans) in remote antiquity, the current Indian populations (both north and south Indian) derive from admixture of ANI and ASI, and not by admixture from any third population. It is the Ancient Europeans which derived from Ancestral North Indians.


The family-tree (Fig 4 of Reich) is good. Yet it does not take into account the dates and places. It should be noted that ANI and ASI are past populations, and hence need to be placed nearer the source than the YRI (Africa), CEU (Europe, Central Asia, West Asia) and Onge (Andaman) populations, which are contemporary living populations. Therefore the picture needs to be corrected, to adjust placing for time. Then the picture would look like this:

Reich 2


However we know, that the stem of the non-African limb of the graphic was located in South Asia. Hence the real picture would be like this:


Reich 3



However, this model ignores the fact that many other populations than the CEU and Ongan had been derived from ANI and ASI. Hence the picture needs to be modified further to accommodate modern north Indian and South Indian populations:


Reich 4

This picture is consistent with both the important conclusions of the Reich’s article:

  1. “These results do not mean that the Indian groups descend from mixtures of European and Austro-Asiatic speakers, but only that they derive from at least two different groups that are (distantly) related to CEU and Santhal.” (Riech et al, p. 4, column 1). This rules out any admixture of Europeans and Austro-Asiatics.


  1. “Applying our model-fitting procedure, we find that the tree (YRI,((CEU,ANI),(ASI, Onge))) provides an excellent fit to the data from Indian groups.”the tree (YRI,((CEU,ANI),(ASI, Onge))) provides an excellent fit to the data” (, p. 4, col 1).


Hence a full synthetic figure would be like this:



Reich 7


At the end it is useful to add that often statements by great authors are best not forgotten. Western Eurasia was formed of populations migrating from Asia and during recent Neolithic times from Africa. Hence if plotted, European genes cannot form any cline towards Asia or Africa, while African and Asian genes will always show clinal pattern of expansion into Europe.


The seminal words of Cavalli-Sforza remain valid even today, “…both Africans and Asians contributed to the settlement of Europe, which began about 40,000 years ago. It seems very reasonable to assume that both continents nearest to Europe contributed to its settlement, even if perhaps at different times and maybe repeatedly. It is reassuring that the analysis of other markers also consistently gives the same results in this case. Moreover, a specific evolutionary model tested, i.e., that Europe is formed by contributions from Asia and Africa, fits the distance matrix perfectly (6). In this simplified model, the migrations postulated to have populated Europe are estimated to have occurred at an early date (30,000 years ago), but it is impossible to distinguish, on the basis of these data, this model from that of several migrations at different times. The overall contributions from Asia and Africa were estimated to be around two-thirds and one-third, respectively”. (Cavalli-Sforza 1997:7720).

The End