Zarathushtra and his steppe posse

Part of the introduction to the new Lopez et al. preprint on the genetics of Zoroastrians says this:

The Zoroastrian religion developed from an ancient religion that was once shared by the ancestors of tribes that settled in Iran and northern India. It is thought to have been founded by the prophet priest Zarathushtra (Greek, Zoroaster). Most scholars now believe he lived around 1200 BCE, at a time when the ancient Iranians inhabited the areas of the Inner Asian Steppes prior to the great migrations south to modern Iran, Afghanistan, Northern Iraq and parts of Central Asia.

Disappointingly, in the rest of the preprint we hear nothing about these great migrations from the Eurasian Steppe and if perhaps they brought at least some of the ancestors of modern-day Zoroastrians to what is now Iran.

The preprint's title, The genetic legacy of Zoroastrianism in Iran and India: Insights into population structure, gene flow and selection, makes it clear that the authors are focusing on the genetic legacy of the Zoroastrians. OK, but why not also expand the focus to a detailed analysis of their genetic origin?

Possibly there's another paper on the way on the genetic origin of the Zoroastrians and other Indo-Iranians? Perhaps, but I'd say the issue here is that the authors have decided to make their main points with haplotypes, rather than unlinked SNPs, probably because, in principle, haplotypes are more powerful than unlinked SNPs.

Thus, they've chosen to limit themselves to using only a few relatively high quality, ancient genomes as reference samples. However, none of these ancient genomes are from the Eurasian Steppe.

As a result, the preprint includes a set of technically powerful haplotype analyses that, unfortunately, say nothing about the potential steppe origin of the Zoroastrians and are generally very difficult to interpret.

To fix this problem they can either sequence a couple of relevant ancient samples from the steppe at a high enough coverage to be useful as reference samples in haplotype tests, and/or expand their use of formal statistics to model Zoroastrians with the already available pseudo-haploid ancients from the steppe (see here).

Actually, since the Iranian Zoroastrians from this study are available online courtesy of Broushaki et al. 2016, I can try some formal statistics models now, using the latest qpAdm and the updated qpAdm methods from Lazaridis & Reich 2017. The results are sorted by statistical fit, best to worst:

Yamnaya_Kalmykia + Anatolia_ChL + Han + Iran_N

Sarmatian + Anatolia_ChL + Han + Iran_N

Afanasievo + Anatolia_ChL + Han + Iran_N

Poltavka + Anatolia_ChL + Han + Iran_N

Scythian + Anatolia_ChL + Han + Iran_N

Potapovka + Anatolia_ChL + Han + Iran_N

Yamnaya_Samara + Anatolia_ChL + Han + Iran_N

Andronovo + Anatolia_ChL + Han + Iran_N

Sintashta + Anatolia_ChL + Han + Iran_N

Srubnaya + Anatolia_ChL + Han + Iran_N

Not a huge difference there in terms of the fits. The best model is with Yamnaya_Kalmykia, probably because of its highest ratio of southern ancestry amongst these ancient steppe herder and warrior groups. Interestingly, the next best model is with the early Sarmatians from Pokrovka, Russia, who were, in all likelihood, Iranian-speakers.

I've also tested many other models using ancient Near Eastern reference samples other than Anatolia_ChL (Anatolia Chalcolithic), and can say with some confidence that the Zoroastrians have, one way or another, ~20% ancient steppe-related ancestry.

But how do other Iranian groups compare? It's an interesting and important question, because if modern-day Zoroastrians harbor elevated ancient steppe-related ancestry compared to other Iranians, this would strengthen the case for the steppe origin of Zarathushtra and his early followers. Let's test this using the same Sarmatian model as above (except with Yoruba added for the Bandaris to account for their minor African admixture):

Iranian_Bandari 27.7±0.6.5%

Iranian_Fars 22.2±4.6%

Iranian_Jew 2.9±0.5.9%

Iranian_Lor 15.3±5.5%

Iranian_Mazandarani 19.9±5%

Iranian_Persian 20±5.1%

And just to see what happens:

Iran_Chalcolithic 0%

So the Iranian Jews and Chalcolithic farmers from Iran basically show 0% Sarmatian-related ancestry. On the other hand, non-Jewish and non-Zoroastrian Iranians harbor, on average, 21.02±5.34% Sarmatian-related ancestry. That's actually not significantly different from the Zoroastrian result of 25.7±4.7%.

But importantly, modern-day Zoroastrians certainly don't appear to fall short in this regard compared to other ethnic and/or regional Iranian groups, despite being a relatively strong genetic isolate for many generations. What this suggests is that the Sarmatian-related ancestry mostly arrived south of the Caspian sometime between the Chalcolithic and the rise of Islam in Iran, quite possibly with the early followers of Zarathushtra during the Iron Age.

Citation...

Lopez et al., The genetic legacy of Zoroastrianism in Iran and India: Insights into population structure, gene flow and selection, bioRxiv, Posted April 18, 2017, doi: https://doi.org/10.1101/128272

Update 30/04/2018: Lots of new ancient samples have arrived, so it's time to revisit this issue. See here.

Zoroastrian preprint (Lopez et al. 2017)

A new prerpint on the genetic legacy of the Zoroastrians has just appeared at bioRxiv. I'm reading it now. Might make some comments later [Update 20/04/2017: Zarathushtra and his steppe posse]. Here's the abstract:

Zoroastrianism is one of the oldest extant religions in the world, originating in Persia (present-day Iran) during the second millennium BCE. Historical records indicate that migrants from Persia brought Zoroastrianism to India, but there is debate over the timing of these migrations. Here we present novel genome-wide autosomal, Y-chromosome and mitochondrial data from Iranian and Indian Zoroastrians and neighbouring modern-day Indian and Iranian populations to conduct the first genome-wide genetic analysis in these groups. Using powerful haplotype-based techniques, we show that Zoroastrians in Iran and India show increased genetic homogeneity relative to other sampled groups in their respective countries, consistent with their current practices of endogamy. Despite this, we show that Indian Zoroastrians (Parsis) intermixed with local groups sometime after their arrival in India, dating this mixture to 690-1390 CE and providing strong evidence that the migrating group was largely comprised of Zoroastrian males. By exploiting the rich information in DNA from ancient human remains, we also highlight admixture in the ancestors of Iranian Zoroastrians dated to 570 BCE-746 CE, older than admixture seen in any other sampled Iranian group, consistent with a long-standing isolation of Zoroastrians from outside groups. Finally, we report genomic regions showing signatures of positive selection in present-day Zoroastrians that might correlate to the prevalence of particular diseases amongst these communities.

Lopez et al., The genetic legacy of Zoroastrianism in Iran and India: Insights into population structure, gene flow and selection, bioRxiv, Posted April 18, 2017, doi: https://doi.org/10.1101/128272

Population geneticists often not very good at population genetics

An abstract book from a recent mathematics meeting in Estonia includes an abstract on the genetic impact of Bronze Age steppe pastoralists on Europe and South Asia. Titled A Pre-Existing Isolation by Distance Gradient in West Eurasia May Partly Account for the Observed “Steppe” Component in Europe, it's mostly authored by scientists from the Estonian Biocentre including Luca Pagani and Mait Metspalu. You can read it here.

Even though it's just an abstract of a paper that might never be published, it's so obviously wrong that I can't let it go. This is the sort of thing I'd expect to see from some of the half deranged visitors in the comments section at this blog, not scientists from the Estonian Biocentre.

First of all, even though the abstract doesn't spell out which data crunching algorithms were used by the authors, it's pretty clear to me that the main part of their analysis was run with ADMIXTURE. That basically makes it a pointless exercise from the outset, simply because ADMIXTURE is not designed for these types of analyses.

Why? Because it's impossible to accurately recapitulate ancient population structure with ADMIXTURE; the results are always significantly skewed in some way, usually by heavy genetic drift in one or more of the test populations. In other words, there's no way to truly revive ancient populations with ADMIXTURE components. And if you can't do that, then how can you estimate their impact more or less accurately? Not possible.

In any case, whether the authors relied on ADMIXTURE or not is immaterial to the fact that all of their main points are clearly wrong. Before I go through these points, and explain why they're wrong, I need to explain exactly what the Steppe component really is and isn't.

The Steppe component is the genetic structure of Early and Middle Bronze Age (EMBA) steppe pastoralist groups Afanasievo, Poltavka and Yamnaya. And it's a very specific thing. It isn't a component inferred from a random run of ADMIXTURE that peaks in Afanasievo, Poltavka and/or Yamnaya, or any other ancient populations.

So, Steppe component = Afanasievo, Poltavka and Yamnaya, or Steppe_EMBA. Nothing more, nothing less. Certainly nothing from outside of the steppe predating Afanasievo and Yamnaya.

Keep in mind also that Steppe_EMBA is a very specific mixture of older and contemporaneous populations. Using the formal-statistics-based qpAdm method, which models ancestry directly based on f4-statistics, Steppe_EMBA is probably best modeled as a mixture of Eastern European Hunter-Gatherers (EHG), Caucasus Hunter-Gatherers (CHG), and Anatolia Chalcolithic (Anatolia_ChL), with ancestry proportions of around 0.453, 0.453 and 0.094, respectively. See here.

I believe that in this model Anatolia_ChL represents some type of minor western admixture amongst the close relatives of CHG still living in the Caucasus during the Eneolithic/Early Bronze Age, and/or minor gene flow from the Balkans onto the steppe. But that's a topic for another day, perhaps after the release of the Bell Beaker behemoth?

Below is a visual representation of the model, using a typical Principal Component Analysis (PCA) of Western Eurasian population structure. Note the tight cluster formed by the Steppe_EMBA groups and individuals, which is easily differentiated from all ancient populations outside of the steppe, except, importantly, Corded Ware.

Thus, considering that I know what the Steppe component is and isn't exactly, then I can try to test for admixture from it and its ancestral components as best I can using qpAdm. Below are results for a few pertinent ancient populations (no idea how to model the farmers from Early Neolithic Iran at this stage, but I've already underlined their unique genetic character here and have no reason to believe that they're responsible for any part of the Steppe_EMBA signal in Europe or South Asia). If you're wondering why I chose Hungary_HG as the potential Western Hunter-Gatherer source, it's because it provided the best statistical fits overall. Also note that Ukraine_HG/N is based on samples from the Pontic Steppe.

CHG

Germany_MN 1
Germany_MN 2

Iran_ChL 1
Iran_ChL 2

Karelia_HG 1
Karelia_HG 2

Latvia_HG 1
Latvia_HG 2

Latvia_MN 1
Latvia_MN 2

Ukraine_HG/N 1
Ukraine_HG/N 2

The models involving Steppe_EMBA and CHG are almost always worse than the best models without them. As far as I can see, there's no strong evidence here of any mixture from a population even similar to Steppe_EMBA in any of these groups, except perhaps Ukraine_HG/N.

However, qpAdm results are dependent on the choice of pright and pleft populations (outgroups and potential mixture sources, respectively). Therefore, with different pright and pleft populations it might be possible to model all of the above groups with significant Steppe_EMBA admixture.

But of course there are other tests that I can run to double check my qpAdm models, such as the West Eurasian PCA. And clearly, the PCA basically supports the qpAdm results, with none of the test groups showing much, if any, deviation towards Steppe_EMBA or CHG from their main mixture clines.

So now let's take a look at the key points made in the abstract and why they're so way off the mark:

However ancient DNA samples from East European and Caucasian Hunter-Gatherers as well as from Early Iranian Neolithic, dating from before the Yamnaya expansion, already show signs of this so called “Steppe” component (Lazaridis et al. 2016).

There's no persuasive evidence for this; see my qpAdm and PCA models above for CHG and various Eastern European Hunter-Gatherer groups. As for the Early Neolithic farmers from Iran, there are no formal models that really make sense for them; we probably don't yet have old enough Near Eastern genomes to serve as potential mixture sources. But the idea that they're somehow interchangeable with Steppe_EMBA is patently idiotic.

Such an observation is compatible with the presence of a pre-existing genetic gradient ranging from Caucasus/Iran all the way to Europe, which likely formed through isolation by distance over thousands of years.

It's not. Isolation by distance has nothing to do with it, because there's no persuasive evidence for the existence of Steppe_EMBA ancestry, or even anything similar, outside of the steppe until the Late Neolithic/Early Bronze Age (LNBA). All of the evidence available to date points to a sudden, massive and perhaps even violent explosion of Steppe_EMBA peoples deep into Europe and also across much of Asia during the LNBA.

Here we show that such a gradient, defined as decrease of "steppe” component with distance from Iran, can be inferred from ancient samples pre-dating the Yamnaya expansion (r^2 = 0.93).

Not possible, because, as I've just pointed out, pre-Bronze Age samples from Iran (Iran_ChL) do not show strong evidence of Steppe_EMBA ancestry aka. the Steppe component.

When analysed in the light of this gradient, later ancient and modern samples from Europe still display an excess of Steppe component, however this excess is less pronounced than previously estimated.

Horseshit. Nothing's changed.

Additionally we found that, of the analysed samples, modern South Asians show the highest excess of “steppe” component, pointing to the documented, recent links between the Caucasus/Iran populations and the South Asian peninsula.

No, you're conflating Steppe_EMBA ancestry with Neolithic ancestry from what is now Iran because you don't know how to differentiate them. But this has already been done many times over on this blog and also in scientific literature.

...

By the way, Iosif Lazaridis made a couple of observations related to the Pagani et al. abstract on Twitter. See here and here.

I suspect P10: http://www.karger.com/Article/PDF/469638 … conflates Caucasus/Iran-component with "steppe" ancestry 1/n

Steppe ancestry brought into mainland Europe post-5kya was a mix of Caucasus/Iran-component (Basal Eurasian-rich) with ANE/EHG-component 2/n

See also...

Globular Amphora people starkly different from Yamnaya people