Y haplogroup R1a is known as the Aryan gene. The Indo Iranian branch of the Indo Europeans who inhabit Iran, Afghanistan, Pakistan and northern India identified themselves as Aryans. Strangely the purest form of Aryans lived and are still living in in Russia and Eastern Europe but they are called as the Slavs.

The Aryans of Iran, Afgh, Pak and Ind are no more pure Aryans as majority of their genes is non Aryan because of further invasions and heavy mixing with the local population. In north India mixing with the local population (the Dravidians) has reduced the proportion of R1a overall to 25%.

Proto-Indo-Iranian speakers, the people who later called themselves 'Aryans' in the Rig Veda and the Avesta, originated in the Sintashta-Petrovka culture (2100-1750 BCE), in the Tobol and Ishim valleys, east of the Ural Mountains. It was founded by pastoralist nomads from the Abashevo culture (2500-1900 BCE), ranging from the upper Don-Volga to the Ural Mountains, and the Poltavka culture (2700-2100 BCE), extending from the lower Don-Volga to the Caspian depression.

The Sintashta-Petrovka culture, associated with R1a-Z93 and its subclades, was the first Bronze Age advance of the Indo-Europeans west of the Urals, opening the way to the vast plains and deserts of Central Asia to the metal-rich Altai mountains. The Aryans quickly expanded over all Central Asia, from the shores of the Caspian to southern Siberia and the Tian Shan, through trading, seasonal herd migrations, and looting raids.

Horse-drawn war chariots seem to have been invented by Sintashta people around 2100 BCE, and quickly spread to the mining region of Bactria-Margiana (modern border of Turkmenistan, Uzbekistan, Tajikistan and Afghanistan). Copper had been extracted intensively in the Urals, and the Proto-Indo-Iranians from Sintashta-Petrovka were exporting it in huge quantities to the Middle East. They appear to have been attracted by the natural resources of the Zeravshan valley for a Petrovka copper-mining colony was established in Tugai around 1900 BCE, and tin was extracted soon afterwards at Karnab and Mushiston. Tin was an especially valued resource in the late Bronze Age, when weapons were made of copper-tin alloy, stronger than the more primitive arsenical bronze. In the 1700's BCE, the Indo-Iranians expanded to the lower Amu Darya valley and settled in irrigation farming communities (Tazabagyab culture). By 1600 BCE, the old fortified towns of Margiana-Bactria were abandoned, submerged by the northern steppe migrants. The group of Central Asian cultures under Indo-Iranian influence is known as the Andronovo horizon, and lasted until 800 BCE.

The Indo-Iranian migrations progressed further south across the Hindu Kush. By 1700 BCE, horse-riding pastoralists had penetrated into Balochistan (south-west Pakistan). The Indus valley succumbed circa 1500 BCE, and the northern and central parts of the Indian subcontinent were taken over by 500 BCE. Westward migrations led Old Indic Sanskrit speakers riding war chariots to Assyria, where they became the Mitanni rulers from circa 1500 BCE. The Medes, Parthians and Persians, all Iranian speakers from the Andronovo culture, moved into the Iranian plateau from 800 BCE. Those that stayed in Central Asia are remembered by history as the Scythians, while the Yamna descendants who remained in the Pontic-Caspian steppe became known as the Sarmatians to the ancient Greeks and Romans.

The Indo-Iranian migrations have resulted in high R1a frequencies in southern Central Asia, Iran and the Indian subcontinent. The highest frequency of R1a (about 65%) is reached in a cluster around Kyrgyzstan, Tajikistan and northern Afghanistan. In India and Pakistan, R1a ranges from 15 to 50% of the population, depending on the region, ethnic group and caste. R1a is generally stronger is the North-West of the subcontinent, and weakest in the Dravidian-speaking South (Tamil Nadu, Kerala, Karnataka, Andhra Pradesh) and from Bengal eastward. Over 70% of the Brahmins (highest caste in Hindusim) belong to R1a1, due to a founder effect.

Maternal lineages in South Asia are, however, overwhelmingly pre-Indo-European. For instance, India has over 75% of "native" mtDNA M and R lineages and 10% of East Asian lineages. In the residual 15% of haplogroups, approximately half are of Middle Eastern origin. Only about 7 or 8% could be of "Russian" (Pontic-Caspian steppe) origin, mostly in the form of haplogroup U2 and W (although the origin of U2 is still debated). European mtDNA lineages are much more common in Central Asia though, and even in Afghanistan and northern Pakistan. This suggests that the Indo-European invasion of India was conducted mostly by men through war. The first major settlement of Indo-Aryan women was in northern Pakistan, western India (Punjab to Gujarat) and northern India (Uttar Pradesh), where haplogroups U2 and W are the most common today.

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