1. What can possibly explain that the Y-Chromosome bottleneck happened pretty much everywhere in the world, though up to several thousand years apart? It just doesn't does seem to make sense that matriarchical killing of men would peak at very different times all around the world.
This seems to be a two part question:
1) What happened in
all the different regions when the Y-Chromosome bottleneck spiked?
2) What happened in
all those region to reverse the Y-Chromosome bottleneck towards normal levels?
It may be a good idea to further analyze this graph showing the possible timeline of the spike in different regions around the world:

Note that the timeframe displayed here is "thousands of years ago" and not BC/AD. Which means that the bottleneck in Europe shown here was around 4000 BC to 2500 BC (not 5000 BC as I wrote earlier).
SOME INSIGHTS FROM THIS GRAPH
a) The Y-Chromosome bottleneck apparently happened first in the Near East, Southeast & East Asia and South Asia.
b) The bottleneck seems to have lasted the longest in South Asia (6000 BC to 1500 BC) and the Near East (5000 BC to 3000 BC), while being much shorter in all other regions. Is there evidence for matriarchical early farming societies surving much longer in places like India? It seems that the famous
Indus Valley civilization (3300 BC - 1900 BC) existed when the bottleneck in that region was reversing, indicating that this culture was quite different than what came before.
c) The spike happened last in Siberia (although the build-up towards it lasted several thousand years). It was also relatively late in Central Asia (4500 BC), despite the indo-european patriarchical systems spreading in that area early on. The spike in Europe was basically in the middle between the early and late spikes in other regions (3000 BC).
d) What is also interesting is that there is a
second Y-Chromosome bottleneck in Central Asia around 1000-1500 AD. In this case it was almost certainly due to the Mongol invasions of Central Asia and beyond, with the conquerors killing a lot of the male population and raping the women in the conquered regions.
e) The Andes in South America also experienced this Y-Chromosome bottleneck and quick reversal very early on (5000 BC). Being disconnected from the rest of the world, this finding is particularly interesting. It seems to suggest the matriarchical system was spread by Atlantean survivors who went to different parts of the world. And the spike seems to have happened at the time of agriculture first spreading in South America as well, which was supposedly developed independently there.
TWO REASONS FOR THE BOTTLENECK
So it seems that there may have been at least two major causes for the Y-Chromosome bottlenecks. The earliest ones could have been caused by matriarchical societies practicing male infanticide on a large scale.
Since there seems to be evidence that in early farming societies women were mostly doing the farming work while men were apparently mostly responsible for hunting - maybe the fact that farming provided much more food while hunting yielded less and less as the population grew could have been a major reason for limiting the number of males.
Maybe the spike was due to the matriarchical early farming societies recognizing that even farming cannot support an increasing number of people, resulting in "population control" measures. Which apparently still weren't enough, since there was a massive die-off in Europe, for example, starting around 5000 BC - unless it was was caused primarily by plague and not by overpopulation.
The later instances of the Y-Chromosome bottleneck seem to have been more likely due to male dominated conquests where males were killed while women were kept alive, either to be raped or maybe also resulting in a sort of "harem model" in many cases.
SIMILARITIES IN DIFFERENT REGIONS WORLDWIDE
The Y-Chromosome bottleneck and the subsequent reversal seem to coincide with quite a few major changes in the prehistoric world:
- Spread of
farming and permanent settlements instead of earlier nomadic hunting and gathering
- Introduction of the concept of
private property
- Introduction of
monogamy (apparently by the new patriarchical societies)
- More
mobility in some societies due to the domestication of horses and the invention of the wheel
Which of these new developments played a role in the Y-Chromosome bottleneck in all the different regions? Why would farming always result in there being less males who reproduce, unless there was a world-wide spread of a matriarchical system with similar beliefs? It does seem that early societies for some reason believed that women should do farming work while men should be hunting.
REASONS FOR THE REVERSAL OF THE BOTTLENECK
The reversal of the early bottleneck (not counting the much later conquest-related ones in Central Asia) seems to be likely due to:
- Introduction of monogamous families as standard in many cultures (did it happen in South America too?)
- Maybe the initial beliefs that men should only hunt fell away and contributed to the normalization
- Patriarchies probably replaced old beliefs regarding the 'value' of males
- Patriarchy, private property and monogamy seem to have been somewhat intertwined new concepts
It seems that looking more into the prehistory in the Andes around the time of the Y-Chromosome bottleneck there (7000 BC) could yield more insights, since it was a disconnected region and still had the same bottleneck in a similar timeframe to the Eurasian cultures.