Western, Central and Southern Europe had indigenous dark-skinned inhabitants until the Early Neolithic era (c. 8,500 years ago). Scandinavia Eastern Europe, roughly to the east of Lithuania and Romania, was already inhabited by light-skinned native people since the Mesolithic period at least (c. 10,000–15,000 years ago).
The large majority of those dark-skinned aboriginals probably had brown skin, brown wavy hair and blue or green eyes, and they were an offshoot of earlier Paleolithic West Eurasians, or rather, more likely, several distinct West Eurasian groups that blended to form a new European population by the Late Paleolithic era (c. 15,000 years ago) .
The western natives, who were dark-skinned, were overwhelmed by a continent-wide colonization of Europe by light-skinned Anatolian farmers starting roughly 8,500 years ago, and by 7,000 years ago they were already dominant almost everywhere in Europe to the west of central Ukraine and the Baltic countries.
There was certainly some degree of violence, and we know that hunter-gatherer peoples tended to be the losers in a conflict with incoming farmers and pastoralists almost everywhere on earth (see, for a much more recent example, the marginalization and territorial encroachment of Central, Eastern and Southern African hunter-gatherers by Bantu farmers).
But what was really decisive is that farmers tended to increase their numbers much, much faster than hunter-gatherers, so the light-skinned farmers of West Asian origin outbred the dark-skinned hunter-gatherers in centuries or at the latest in a couple of millennia. At first they barely mixed with the indigenous western hunter-gatherers, but those seem to have survived and in parts even thrived in parts of Europe (probably moslty in Northern Europe and Iberia), and they had a sort of resurgence after the Middle Neolithic (c. 7,000 years ago), with their ancestry reappearing in minor but relevant proportions in much of Europe (~15–25% instead of ~0–5%).
By the Late Neolithic, the dark-skinned inhabitants had virtually disappeared as they had mixed too extensively with the light-skinned farmers and had become a minor component in their genetic ancestry. Eventually, in the Late Copper Age and especially in the Early and Middle Bronze Age (c. 3,500–5,000 years ago), the Eastern European (modern Ukraine and Russia) pastoralists, who had indigenous Eastern European and Caucasian ancestry and were also light-skinned, moved en masse into Europe, which probably coincided with or immediately followed a massive plague that crashed the population of many parts of Europe, especially Northern Europe. They mixed with the extant farmers already living there and started to form the present genetic structure of the European continent.
And that’s how the visible signs of the indigenous dark-skinned inhabitants of Europe gradually disappeared, via genetic dilution, outbreeding and immigration. Random long-term genetic drift and gradual natural and sexual selection did the rest of the trick. The descendants of those dark-skinned natives are the modern pale-skinned Europeans, who owe between 5% and 25% of their ancestry to the western hunter-gatherers from Mesolithic Europe, and those who have the largest amount of such ancestry are the Balts:
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