This is going to be rather long and geeky, I'm afraid.
I'm currently reading Who We Are and How We Got Here, by David Reich. It's about discoveries, over the last twenty years or so, concerning the DNA of past populations of humans around the world. It's a fascinating book, and I may give it a review later on, but the chapter I just completed triggered a series of thoughts.
About 5000 years ago, a population originating in the East European steppe, the Yamnaya culture, expanded hugely into Europe, displacing a resident farming population. Part of their success can be attributed to the discovery of the wheel; charioteers made a formidable fighting force against a sedentary, wheel-less population, But there may have been a second factor. Analysis of the teeth of the indigenous farmers, before the Yamnaya expansion, shows no indication of exposure to Yersinia pestis - the plague bacterium - but afterward, both populations show traces of its presence. It is entirely possible that the farmers were decimated by plague, easing the way for the intruders.
What follows is my own reasoning, not Reich's, and if anyone wants to rebut, I'll be glad to read it.
A digression: for a long time, the received wisdom was that disease pathogens undergo evolutionary pressure towards reduced virulence - a host who survives for a long time after infection is more likely to infect others. A generation or so ago, Paul Ewald pointed out that this applies only to diseases spread by personal contact, not to vector-borne diseases; for those, a host does not need to be out and about to spread the disease. (His Evolution of Infectious Disease is also fascinating.)
The reason this comes to mind is this: the Yersinia DNA recovered from the farmer and Yamnaya populations lacks the genes that permit transmission by fleas. The plague outbreak (if such it was) was pneumonic plague - which is directly transmitted, not vector-borne. At that time, then, plague would have been subject to pressure towards reduced virulence, which would allow for mutual adaptation, given enough time, between the Yamnaya and the pathogen, while the farming population would have faced a virgin-field epidemic, rather like the Native Americans at the time of the Columbian Exchange.
Most of the genome of modern Europeans is derived from the Yamnaya; there is relatively little trace of the ancient farmers.