The Near East ain't what it used to be

Up for public comment at bioRxiv this week is this paper on the population history of the Near East, with a special focus on Armenians. Here's the abstract:

The Armenians are a culturally isolated population who historically inhabited a region in the Near East bounded by the Mediterranean and Black seas and the Caucasus, but remain underrepresented in genetic studies and have a complex history including a major geographic displacement during World War One. Here, we analyse genome-wide variation in 173 Armenians and compare them to 78 other worldwide populations. We find that Armenians form a distinctive cluster linking the Near East, Europe, and the Caucasus. We show that Armenian diversity can be explained by several mixtures of Eurasian populations that occurred between ~3,000 and ~2,000 BCE, a period characterized by major population migrations after the domestication of the horse, appearance of chariots, and the rise of advanced civilizations in the Near East. However, genetic signals of population mixture cease after ~1,200 BCE when Bronze Age civilizations in the Eastern Mediterranean world suddenly and violently collapsed. Armenians have since remained isolated and genetic structure within the population developed ~500 years ago when Armenia was divided between the Ottomans and the Safavid Empire in Iran. Finally, we show that Armenians have higher genetic affinity to Neolithic Europeans than other present-day Near Easterners, and that 29% of the Armenian ancestry may originate from an ancestral population best represented by Neolithic Europeans.

Unfortunately, the authors failed to even mention the main cause of what they're seeing; the massive influx of Ancient North Eurasian (ANE) admixture into the Near East. They included ancient genomes Oetzi the Iceman and La Brana-1 in their analysis, but not MA-1 or Mal'ta boy, the main ANE proxy.

MA-1 is a low coverage genome, and not easy to work with, but until better ANE reference genomes are sequenced, it simply can't be ignored in studies on the population history of West Eurasia. Here's why:

Above is my Fateful Triangle PCA. Note the eastern shift of the Islamic Near Eastern groups relative to their non-Islamic neighbors. Here are the relevant ANE ancestry proportions:

Anatolian Turks ~16.54%
Armenians ~15.48%

Iranians ~19.61%
Iranian Jews ~14.01%

Lebanese Muslims ~9.82%
Lebanese Christians ~7.14%

The differences aren't very dramatic, but they're consistent and, as per the PCA, hard to overlook. Indeed, the contrast would be even more obvious if we were to add to the list other exotic admixtures, such as East Asian, South Asian and/or Sub-Saharan.

If you're wondering why it is that Muslims generally carry more ANE than their non-Muslim neighbors, it's probably because the Islamic expansion had a homogenizing effect on the Near East, and it didn't have as much of an impact on the religious minorities in the region.

How and when ANE arrived in the Near East is still a mystery which can only be solved with ancient DNA. However, my bet is that most of it came after the Neolithic from the Eurasian steppe, the northeast Caucasus and the Altai, with the Indo-Europeans, Kura-Araxes people and Turks, respectively.

Citation...

Marc Haber et al., Genetic evidence for an origin of the Armenians from Bronze Age mixing of multiple populations, bioRxiv, Posted February 18, 2015. doi: https://dx.doi.org/10.1101/015396

See also...

First look at an ancient genome from Neolithic Anatolia