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Understanding Reich, David et al, 2009

by P. Priyadarshi
Some findings and their explanations from the research paper: Reich, D. et al 2009, Reconstructing Indian population history, Nature 461:489-494. link: http://www.genome.duke.edu/seminars/journal-club/documents/nature08365.pdf

Paradigms, especially old ones, die harder than Bruce Willis. (James Adovasio 1999)1 Reich et al (2009) was a landmark work for human history. Yet unfortunately very few people gave it an attentive reading. Moreover, there seems to be a wide understanding-gap between the statisticians who worked up the research, and the biologists who wrote the script, and perhaps could not grasp many of the hardcore statistical results (vide infra). This may be called interdisciplinary comprehension gap.

Quoted by Oppenheimer, S. J., 2010, Comment on Donohue, M. and Denham, T.,

Farming and Language in Island Southeast Asia, Current Anthropology 2010, 51(2): 243244.

Indian castes are only 600 years old: One of the important findings of the article is that the Indian caste system is not very old. Reich et al examined six IndoEuropean and Dravidian speaking groups (caste or tribe), and found that their founder event dated back to about thirty generations back (p. 1 pdf). Each generation is considered about 18 to 20 years. Hence these castes were founded about 600 years back. This figure is consistent with findings from history that endogamous caste system started only during the late medieval period in India (Basham:148; It was only in late medieval times that it was finally recognized that exogamy and sharing meals with members of other classes were quite impossible for respectable people.) However the study noted that the Vaishya group had a founder event 100 generations back, i.e. about 2,000 years back. It should be understood that Vaishya is not an endogamous caste, but is a group of about a thousand or more trading groups, each unit group being an independent endogamous caste. Hence this result about the Vaishyas does not tell us anything about the date of origin of the caste system. If more people from Vaishya groups were included, e.g. a few from Tamil Nadu, and a few others from Bengal, their founding event might go back to 20,000 or 30,000 years back. However, from the present result we may assume that the figure 2,000 years reflects the time of founding of trading and commerce guilds, which the term vaishya connotes in modern times. Max Weber and many other authors think that such guilds

came into existence once the emancipatory religions (like Buddhism and Jainism) became strong enough in India (Max Weber:399; 'Guilds' of merchants, and of traders figuring as merchants by selling their own produce, as well as 'craft-guilds,' existed in India during the period of the development of cities and especially during the period the guilds were related.) Indian Population is Indigenous: Reich et al 2009 provided a robust support to Metspalu et al (2004) and Sahoo et al (2006). However because of inattentive, casual and cursory readings of their article by some evolutionary biologists, it has been claimed that Reich et al 2009 contradict some of the findings of Metspalu et al and Sahoo et al. (e.g. Romero et al 2011:21). Thus Romero et al (2011) wrote about Reich et als findings: (a) A recent study has argued for a sizeable contribution from western Eurasia to the ancestral north Indian gene pool (Reich et al. 2009), although it has not provided a date or a precise origin location for this event, and the observation is compatible with low continuous gene flow over a long time period. (Robero et al:20-21 pdf). This reading is atrocious. Reich et al do not even suggest any gene-flow from western Eurasia to South Asia. See discussion below. in which the great salvation religions originated. As we shall see, the salvation religions and

(b)

Another such reading of Reich et al is: However, 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), suggesting that the west Eurasian genetic contribution identified by Reich et al (2009) principally reflects gene flow from Iran and the Middle East. (Robero et al:21 pdf). This conclusion too is atrocious. This statement (by Robero et al) implies presence of west Eurasian genes in Iran and Middle East, and also their flow into India to the extent that they are detectable today in India: a conjecture (see Renfrew 1989; Bellwood 2005 etc), which has been explicitly ruled out by Sahoo et al (2006:847), and many other authors. Sahoo et al had actually written the following words: The perennial concept to of India people, language, through and the agriculture arriving together

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.

Kivisilds 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. 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. Thus Romero et al have invented something and labelled it to have been written by Reich et al, and then arrived at a compromise that there was a migration of West Eurasian genes from Iran/ Middle East to north India. Thus any discord between Sahoo et al and Reich et al, or that between Kivisild et al and Reich et al etc is in fact nonexistent, and is a product of misreading by a fertile brain. Incidentally, Reich is a co-author of Robero et al! Hence it is important that Reich et al must be well explained to readers. An attempt to which is being made below.

Understanding Reich et al 2009

The things we just saw have happened only because Paradigms, especially old ones, die harder than Bruce Willis (James Adovasio 1999; quoted by Oppenheimer 2010). It is therefore desirable that Reich et al 2009 should be explained in more simple English once more so that casual readers may not get confused.

Reich et al never said that there was any flow of west Eurasian (European) gene into South Asia. To prevent such misleading readings of their article, they explicitly mentioned: 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), however it means a common ancestor for both ANI 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 can be seen at the link below:
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2842210/figure/F4/ or, http://www.nature.com/nature/journal/v461/n7263/fig_tab/nature08365_F4.html 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:

Original Human Population in Africa

ANI

Africa Europe (YRI) (CEU) contemporary

ASI Hypothetical, remote past Andaman Populations (Onge, of North India contemporary) and South India respectively

The top inset from Stephen Oppenheimers 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). It does not say that different Indian groups have inherited different proportions of ancestry from the CEU and However, this latter is the impression, Romelo et al have derived from Reichs article! Here we note that, in spite of the fact that ANI were related to Western 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. Contrary to this clear finding, Romero et al read from this paragraph, the observation is compatible with low continuous gene flow over a long time period (p. 21 pdf, last line) [into South Asia from Europe or West Asia: square bracket added.] This is atrocious. It may be noted that neither Reich et al, nor any other worker has ever claimed low continuous gene-flow into Indian sub-continent from any outside source/place. Now we can come back to the family tree. The family-tree (Fig 4 of Reich) is good. Yet it does not take into account the dates. It should be noted that ANI and ASI are past populations, and hence need to be placed nearer the source than the YRI, CEU and Onge 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:

Original Population

CEU Europe Modern

However, from Metspalu (2004) and many other studies, 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:

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Original Population

ASI

CEU Europe

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:

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Original Population

Ancestral African

Ancestral Indian First Out of Africa arrival into India/ or the relic Indian Population after Toba eruption

Ancestral North Indian; in north India

Ancestral South Indian; in south India

ONGAN Andamane se Tribes

CEU Modern Eur

YRI West Africa etc

Modern South Indian Population

This picture is consistent with both the important conclusions of the Reichs article:

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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. 2. 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 (Ibid., p. 4, col 1). Hence a full synthetic figure would be like this: Original Human Population in Africa

Location: India Location: Location: India India /East Iran

ASI (Located in South India long back) Africa Europe (YRI) (CEU) contemporary
Modern North and South Indian populations Andaman as an admixture of ASI and ANI (Onge)

Pathan, Vaishya, contemporary Meghawal, Bhil, Contemporary.

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Problem of Adyegi: Reich et al note (p. 4 pdf): the ANI and CEU form a clade, and further analysis shows that the Adygei, a Caucasian group, are an out-group Indian and European groups speak IndoEuropean languages, whereas the Adygei speak a Northwest Caucasian language. This issue can be resolved by assuming that the Adyegi broke off from north Indian population just before split between ANI/CEU. This split as well as the ANI/CEU split must have occurred before LGM. It is also helpful to remember that the modern languages of Europe are products of language change from elite dominance by incoming farmers. There has been population replacements too, either coming through northeastern corridor of Europe, or through the Balkans-West Asia route. Hence the ANI-CEU clade may not have spoken the Proto-Indo-European, rather they possibly spoke the Proto-Nostratic. Ancestral Europeans spoke Semitic and other languages, but not the Indo-European (Baldi and Page, 2003). Proto-Indo-European evolved within the ANI population after split from CEU. ANI-ASI admixtures took place after LGM. If we add these few understandings to the findings of Reich et al 2009, it becomes much more comprehensible and fits other stories well. 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 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.

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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). This explains Reich et als finding that The most remarkable

feature of the PCA is a gradient of proximity to western Eurasians (Supplementary Fig. 5), an analogous PCA in Europeans did not produce a gradient of proximity to India (p. 3 pdf) This finding too is consistent with our knowledge from other sources. European population has been derived from north African, West Asian, Central Asian, and through the latter the Indian source. Caucasian and Palaeolithic genes too have contributed to making of modern Europe. Hence its clines are distorted, and a gradient of proximity to India cannot be produced. However, from India, genes spread like advancing waves, hence clinal rings could be formed. However if we are imaginative enough to visualize the wave- like picture of a clinal wave, we can appreciate that only the source

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population can have the waves of expansion as a cline. This makes obvious that Europe was not the source of any population in the world, but rather a recipient of DNAs from other parts of the world.

References:
Baldi, P. and Page, B.R., Europa Vasconica-Europa Semitica Theo Vennemann, Gen. Nierfeld, in: Patrizia Noel Aziz Hanna (Ed.), Trends in Linguistics, Studies and Monographs 138, Mouton de Gruyter, Berlin, 2003, pp. xxii + 977

Basham, A.L., The wonder that was India, Third revised ed (1967), thirty-fifth impression, 1999, Rupa and Co., Bombay.

Cavalli-Sforza, L.L., 1997, Genes, Peoples, and Languages, PNAS, 94(15):7719-7724.

Kivisild, T. et al, The genetic heritage of the earliest settlers persists both in Indian tribal and caste populations, Am J Hum Genet, 2003 Feb, 72 (2) : 313-32.

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Metspalu, M. et al, 2004, Most of the extant mtDNA boundaries in South and Southwest Asia were likely shaped during the initial settlement of Eurasia by anatomically modern humans, BMC Genetics 2004, 5: 26doi:1186/1471-2156-5-26 Reich, D. et al, 2009, Reconstructing Indian population history, Nature 461:489-494. Romero, I.G. et al, 2011, Herders of Indian and European cattle share their predominant allele for lactase persistence, Molecular Biology and Evolution, Advance Access Published August 11, 2011. Sahoo, Sanghmitra et al; A prehistory of Indian Y chromosomes: Evaluating demic diffusion scenarios, PNAS 2006, 103(4): 843-848. Weber, Max, Gerth, H. H. and Turner, B. S., India: The Brahman and the castes, in From Max Weber: Essays in Sociology, Routledge, 1991. First published in 1921 in German as Part 3, Chapter 4 of Wirtschaft und Gesellschaft. English translation by Girth, H. H. and Mills, C. W., as Class, Status, Party. Pages 180195 in From Max Weber: Essays in Sociology, Oxford Univ. Press, New York, 1941, 1958.