The true source of the steppe ancestry in modern Indians

 

This post aims to clarify the source of the bronze age steppe ancestry in modern Indians. For this, I have chosen the following targets.

Modern targets and their details

Mitanni at Hasanlu - Did they have Sintashta ancestry or not?

I want to make a quick post on a new article by Nezih Seven. You can find it here.

A Genetic Analysis of Historical Population Movements Around The Zagros Mountains

He analyzed the NW Iranian samples from the 'Southern Arc' paper and reached some interesting conclusions.

Model for Hasanlu_LBA_A by Nezih

The p-value of the above model is ~0.20 (therefore passing as p>0.05). His qpAdm output file can be seen here. 

Ancestry trends of 150+ groups from the Indian subcontinent

In this article, I will lay out general ancestry trends of 150+ groups from the Indian subcontinent. And try to make it make sense to a lay audience.

Before I present the data table, there are some important caveats:

1. The purpose of the table is to concurrently compare the ancestry trends for 100+ groups of the Indian subcontinent. If the chosen sources are incorrect, they will be incorrect for all the groups but will still allow us to compare ancestry % across groups and make some conclusions. The fit (distance %) is not too relevant, and the distances of some groups will indeed be bad (>3%). However, that does not take away from our purpose of finding broad trends within the data.

Did Y haplogroup R1a-Y3 go into hiding?

 

As per the Harvard database, there are 454 male samples dated between 3000BCE and 0CE in all the *stan countries north of India and Russia combined. Of these, 166 are R1a but none is R1a-Y2 or L657+ which is supposed to have been formed around 2600BCE from Steppe R1a-Z94 > Y3.

In Narasimhan et al 2019 supplement too, there are 250 male samples analyzed between the dates 3000BCE - 0 CE, and none of them is R1a-Y3+. These include all the Sintashta, Andronovo, Saka and descended culture samples, all of these have significant steppe_mlba admixture.

This is the modern country-wise frequency of R-Y3+ lineages as per YFull (23 countries, 13250 samples). As you can see, only the Indian subcontinent sees R1a-Y3+ samples, with an average of ~15-20% of all males sampled in Pakistan, India, Nepal, Bangladesh and Sri Lanka. The only thing common between these and the steppe R1a is a common ancestor who lived around 2600BCE. But if his descendant Y3 was born in the steppe, we should have seen much more Y3 in the ancient samples and in the modern distribution in the countries north of India. So where are they?

R1a Explained

Y Haplogroups - A Primer

Y Chromosome haplogroup is a defined set of mutations in the (non-recombinant) portion of the DNA from male specific Y-chromosome. Y-Chr is passed down from father to son along with all the mutations that have been accumulated till that point. All the male descendants of a man will share the mutations in the Y-Chr of that man, plus all the additional mutations that have been collected in the generations between that man and the descendant on his specific male ancestral lineage chain. This feature helps us in identifying the most recent common paternal ancestor of a group of men and is a great tool for population geneticists. Do note that the same set of additional mutations cannot be created in two different men at the same time, the probability of that happening randomly is 0.

mtDNA haplogroups are mutations found in the mitochondrial DNA. Unlike autosomal chromosomes and Y chromosomes, mtDNA is found outside the cell nucleus. mtDNA is passed down from mother to children only, and therefore is informative only of the maternal lineage of a person. 

In this article, we will discuss Y haplogroups which can only inform us of the paternal ancestry of males.

Exploring the sources of the 'Southern ancestry' in the Steppe

The proximal source of the southern (IranN/CHG) ancestry in the Eneolithic Steppe as well as Yamnaya populations has been a mystery. Chintalapati et al 2022 infer that the admixture between Eastern European Hunter-Gatherers and Iran Neolithic ancestry occurred between 4400-4000BCE, using the DATES algorithm developed by Moorjani Lab.

In this post, powered with newly published samples as well as better tools than before, I will attempt to decipher the true sources of these populations.

Disclaimer: The analysis presented below is based on the currently available published samples from the Pontic Caspian Steppe. The samples from the Middle Don region (Allentoft et al 2022 preprint) are unavailable, and this analysis will be updated once those samples become available.

The Lady from Central Asia who was found dead in a Bronze Age Turkish well

 

Site of the Alalakh 'Well Lady'. Courtesy: Skourtanioti et al 2020

The remains of the Alalakh 'Well Lady' were discovered in the archaeological site of Tell Atchana / Alalakh / Alalah, Turkey dating to ~1550BCE. Her aDna was published in 2020 (1) and she was found to be of central Asian origin, far from where she was found. She was found at the bottom of a deep well that was still in use at the time. The individual showed evidence of healed trauma on the skull's frontal bone and two healed fractured ribs, and her manner of death has been suggested as a homicide due to or before being thrown into the well (2). Her teeth also showed clear signs of enamel defects (2), a possible sign of malnutrition during childhood. Her age at death was 40-45 years.