Agriculture and cities brought many changes, but not all of them were good. Two things in particular led to problems: irrigation and domestication of animals. The problem with irrigation was that it was transforming a naturally hot and dry environment into a hot and wet one. This brought with it a number of water-borne parasites native to the area, such as the blood fluke that causes Schistosomiasis by burrowing into the skin, entering a new larval stage (schistosomula), then migrating to the liver or lungs, where it matures into the adult form. The overall effect for a society heavily infected with such diseases was a lethargic peasantry unable to produce as much or fight as well against invading enemies.
The second, and more dramatic effect came with the domestication of animals and the subsequent frequent contact with them, because microbes for infectious diseases the animals carried often mutated into forms that were lethal to humans. There are at least 26 diseases we share with poultry, 35 with cattle, 42 with pigs, 46 with sheep and goats, 35 with cattle, 50 with horses, 65 with dogs, and even 32 with rats and mice who typically live in close proximity with humans. The first outbreaks of any of these diseases were often catastrophic, since people had no prior exposure to them and thus had no chance to develop immunities.
The rise of cities was both good news and bad news in this respect. The good news was that the more concentrated populations made possible by cities meant that despite the huge mortality, at least a small percentage of the population could survive and develop resistance to the new disease. The bad news was that the civilization would be more vulnerable to attack by enemies.
In the long run, two things helped populations to develop at least partial immunity to diseases. One was that natural selection favors people with natural resistance to the disease, so they can pass that resistance on to future generations. By the same token, natural selection favors organisms less lethal to their hosts so that they don’t have to keep looking for new hosts in order to survive. Therefore the more lethal strains of a disease will typically reach a dead end, literally, when it has killed off all its potential. After six generations or so, a population was able to adapt enough to keep damage from new outbreaks of a disease from doing too much harm. Oftentimes, the disease becomes a chronic, but less lethal “childhood” sickness that, once people have had it, usually as children, they are immune to any recurrence. Even in their less lethal chronic state, such diseases can have dramatic effects in three ways.
First of all, once adapted to a disease, a civilization could turn it into a lethal weapon, although usually unknowingly, since people didn’t understand what caused diseases until the 1800s. Still, people from a civilization could carry a disease to other previously uninfected populations, in particular nomads. This would have one of two results. Either it would virtually wipe out the nomads whose small populations could not sustain the disease long enough to adapt to it. Probably the most dramatic instance of this happening was when Europeans brought infectious diseases, such as smallpox, to the Americas. Within a century, as much as 90% of the Native American population had perished, mostly from European diseases.
On the other hand, the nomads might manage to adapt to the disease and eventually conquer the civilization. The ability to sustain the necessary numbers might come from civilized women captured in raids who could pass on their immunity to their children.
A second effect was that even in their less lethal form, diseases would still kill some people in the cities. Compounding this was the cramped and filthy living conditions typically found in pre-industrial cities. Together these would often prevent cities from sustaining their populations through natural increase. Therefore, people from the countryside and beyond that state’s borders would migrate there looking for job opportunities, and often finding them as a result of disease killing previous residents. If something happened that drastically reduced the city’s population, there could be a sudden influx of foreign migrants who might replace the older civilization’s culture with their own. A likely example of this was the takeover of Sumerian civilization by the foreign Akkadians, not by conquest by infiltration led by Sargon of Kish who held the position of cupbearer to the king.
Finally, there was the effect of civilized diseases on relatively isolated outlying villages that didn’t have the numbers to withstand the initial outbreak of a disease. Such outbreaks would be less frequent, but when they hit, could be much more severe in their effects. An example of this was the American Civil War where big strong soldiers from the countryside died at a much greater rate from diseases than their comrades from the cities who had already been exposed to them and developed some resistance.