Eurogenes Blog: Europe's ancient proto-cities may have been ravaged by the plague
The Cucuteni-Trypillia culture of the Eneolithic Balkans and Eastern Europe is best known for its mega-settlements or proto-cities, each one featuring hundreds of homes, temples and other structures, and likely to have been inhabited by as many as 20,000 people. But from around 3,400 BC these mega-settlements were no longer being built, and a few hundred years later the Cucuteni-Trypillia culture vanished.

Two main explanations have been given for its rather swift demise: violent invasions by steppe pastoralists from the east and/or a massive out-migration by its people as a result of environmental impacts from rapid climate change (see here). However, these theories have failed to gain wide acceptance due to a lack of hard evidence in their support.
Eneolithic = Chalcolithic = Copper Age

At its height, the Cucuteni-Trypillia/Tripolye culture ranged over what is now northern Romania, Moldova, and western Ukraine. It was the height of Neolithic and Copper-Age European sociocultural development. Over a millennium later, well into the Bronze Age, the Minoans had a somewhat similar society on Crete, and in the Americas, people also did impressive achievements with Neolithic technology, like the Aztecs' capital city Tenochtitlan, with a population of 200,000 - 300,000 people with a rather complex system of social classes.

Emergence and Spread of Basal Lineages of Yersinia pestis during the Neolithic Decline: Cell -- the organism that caused the Black Death, a plage that killed some 75 to 200 million people in Eurasia and that killed 1/3 to 1/2 of Europeans over 1347 - 1351. It has also caused several other big epidemics, like the Plague of Justinian (541-542 CE), named after the Byzantine Emperor at that time.

From that paper,
Between 5,000 and 6,000 years ago, many Neolithic societies declined throughout western Eurasia due to a combination of factors that are still largely debated. Here, we report the discovery and genome reconstruction of Yersinia pestis, the etiological agent of plague, in Neolithic farmers in Sweden, pre-dating and basal to all modern and ancient known strains of this pathogen. We investigated the history of this strain by combining phylogenetic and molecular clock analyses of the bacterial genome, detailed archaeological information, and genomic analyses from infected individuals and hundreds of ancient human samples across Eurasia. These analyses revealed that multiple and independent lineages of Y. pestis branched and expanded across Eurasia during the Neolithic decline, spreading most likely through early trade networks rather than massive human migrations. Our results are consistent with the existence of a prehistoric plague pandemic that likely contributed to the decay of Neolithic populations in Europe.

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In this work, we report the discovery of plague infecting Neolithic farmers in Scandinavia, which not only pre-dates all known cases of plague, but is also basal to all known modern and ancient strains of Y. pestis. We identified a remarkable overlap between the estimated radiation times of early lineages of Y. pestis, toward Europe and the Eurasian Steppe, and the collapse of Trypillia mega-settlements in the Balkans/Eastern Europe.