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According to Nyingmapa tradition, the Dzogchen precepts were first expounded in our human world by the Nirmanakaya Garab Dorje (dGa'-rab rdo-rje, Skt. *Prahevajra) in the country of Uddiyana and were later propagated in India by his disciple Manjushrimitra. The latter transmitted them to his diciple Shrisimha who, in turn, conferred them upon Padmasambhava, Vimalamitra, and Vairochana the translator. These three brought the precepts to Tibet in the middle part of the eighth century. Thus, this teaching was originally a secret oral instruction restricted to a small group of Tantric initiates. The tradition claims that it originally came from the mysterious country of Uddiyana to the northwest of India. Therefore, it appears most likely that it is to the Indo-Tibetan borderlands of the northwest that we should look for the origins of Dzogchen. 
This seems equally true for the historical origins of Bonpo Dzogchen, for this second authentic lineage of the Dzogchen teachings also did not originate in India proper, but was brought to Central Tibet in the ninth and tenth centuries from Zhang-zhung in Northern Tibet by the disciples decending from Gyerpung Nangzher Lodpo.  Until the eighth century, the country of Zhang-zhung had been an independent kingdom with its own language and culture. It lay in what is now Western and Northern Tibet and the center of the country was dominated by the majestic presence of the sacred mountain of Gangchen Tise or Mount Kailas. Examining the available evidence, it now appears likely that before Indian Buddhism came to Central Tibet in the seventh and eighth centuries, Zhang-zhung had extensive contacts with the Buddhist cultures that flourished around it in Central Asia and in the Indo-Tibetan borderlands. Just to the west of Zhang-zhung there once existed the vast Kushana empire which was Buddhist in its religious culture. It was an area in which Indian Buddhism interacted with various strands of Iranian religion-- Zoroastrian, Zurvanist, Mithraist, Manichean, as well as Indian Shaivism and Nestorian Christianity. This was also true of the oasis cities of the Silk Route to the northeast of Zhang-zhung such as Kashgar. Some scholars have seen this region beyond India as playing a key role in the development of certain aspects of Mahayana Buddhism, and later also in the development of Tantric form of Buddhism known as Vajrayana.  For example, the revelation of the Guhyasamaja Tantra is said to have occurred to king Indrabhuti in Uddiyana and was later brought to India proper by the Mahasiddhas Saraha and Nagarjuna.  Moreover, the Kalachakra Tantra is said to have been brought from Shambhala in Central Asia to Nalanda in India in the tenth century by the Mahasiddha Tsilupa.  The Bonpos came to identify this Shambhala with Olmo Lungring itself.  All this suggests that certain trends within Yungdrung Bon, rather than being later plagiarisms and imitations of Indian Buddhism concocted in the tenth century, actually do go back to a kind of syncretistic Indo-Iranian Buddhism that once flourished in the independent kingdom of Zhang-zhung before it was forcibly incorporated into the expanding Tibetan empire in the eighth century. This "Buddhism", known as gyer in the Zhang-zhung language and as bon in the Tibetan, was not particularly monastic, but more Tantric in nature and its diffusion was stimulated by the presence of various Mahasiddhas in the region such as the illustrious Tapihritsa and his predecessors dwelling in caves about Mount Kailas and about the lakes to the east in Northern Tibet. Even into this century, Kailas remained an important site of pilgrimage drawing Hindu sadhus and yogis from India. 
Such a mixed "Buddhist" culture, being both Tantric and shamanic, was suppressed in the eighth century when, at the instigation of the Tibetan king Trisong Detsan, the last king of independent Zhang-zhung, Ligmigya, was ambushed and assassinated when he left his castle of Khyung-dzong on the Dang-ra lake in Northern Tibet. Zhang-zhung and its people were absorbed into the Tibetan empire and disappeared as an independent entity. The Zhang-zhung-pas were pressed into the service of the Tibetan army as it expanded westward into Ladakh and Baltistan.  Today the Zhang-zhung-pas survive as the nomad people of Western and Northern Tibet, often possessing the same ancient clan names. But having been converted to the Drigung Kagyudpa school of Buddhism, they have forgotten their ancient heritage. The old caves, once the dwelling places of the Bonpo Mahasiddhas, are now thought to be the domain of ghosts, places to be shunned and avoided. Yet ancient ruins, believed to antedate the Tibetan empire, are still to be seen at Khyung-lung (Khyung-lung dngul-mkhar) west of Kailas and on the shores of the Dang-ra lake to the east in Northern Tibet. 
In response to the urgings of the Indian Buddhist monk-scholar Bodhisattva, who thoroughly rejected these Bonpo heretics,  and failing to recognize the ties of doctrine and practice between the "Buddhism" of Zhang-zhung known as Gyer or Bon, with the monastic Buddhism recently imported from India into Central Tibet, the Tibetan government actively suppressed the indiginous religious culture of Zhang-zhung. Moreover, the persecution of the Bonpos by the Tibetan king Trisong Detsan may have had a political motive and not just a religious one. At that time, the Bonpos in Tibet were certainly not organized into a rival church or sect that could effectively oppose the Indian monks financially supported by the Tibetan government. This picture was a later anachronism created in the accounts of the medieval Buddhist historians. Rather than a conflict of rival religious doctrines, a parallel might be the suppression and subsequent annihilation of the Druids by the Romans in Gaul and Britain, where the Druids represented an ever-present source for Celtic nationalism and rallying point for resistance against Roman rule. In the same way, the Bonpos may also have been suppressed because they represented a possible source of Zhang-zhung-pa rebellion against the rule of the Yarlung dynasty of Tibet. Just as the Druids were accused of making human sacrifices and the Romans used this accusation as an excuse to exterminate them, so the Bonpos were accused of making blood sacrifices and this represented another excuse for expelling them from Tibet.