Bottleneck is the part of a bottle where the material is the thinnest. All the material within the bottle is constricted as it flows out of the bottle controlling the amount of the material coming out. In biology, bottleneck refers to a restriction in the DNA, or the loss of variability within a species.
Some of the great bottlenecks in biology include house cats. House cats are thought to have arisen in Egypt, exclusively. Near the upper Nile there exists a species of wild cat that looks like a house cat in size and shape. When harvests of grain became large, cities develop. The extra grain allows other people to specialize outside of farming and subsistence living. As the harvests get larger more and more people can live not as farmers. When this happens granaries must be built, places to store the excess grain from harvests. However, large stores of grain attract pests and there is nothing that can be done about that. If a granaries lost half of all their grain to pests, half the number of specialists can be maintained.
In comes that cat. Possibly attracted to the granaries due to the concentration of food, the pests that fed on the grain, someone noticed this fact and began attracting more cats to their granary and losses of grain began to be reduced. I imagine that there were still losses, but it was much less. Less grain loss means more specialists. Specialist make clothing, they make tools they improve roadways, all things the farmer used to do, so the farmer has more time now to farm and harvests rise again. Civilization arises, all due to cats.
Granaries are in every land, they all have the same problem. I imagine that the gift of a pair of cats would be a gift that out weighed gold and the cat was spread slowly through the old world, a few cats gave rise to all house cats. That is a bottleneck, the genetic variation of those few wild cats gave rise to all cats, but the wild population of cats in upper Egypt, has greater variation that all house cats, because they were not bottlenecked.
Dogs rose multiple times in multiple locations at multiple times in history. They have more genetic variation than cats because of this fact. As you can see when you compare the number of varieties of either species and the variation in colour, size and shape. People have been selecting for specific traits for millennia, breeding brother to sister to strengthen desired traits. And in humans that is considered crude, rude and obscene, but with dogs or cats no such problem. However, with the desired traits, undesirable traits also arose. For example there are diseases that affect certain breeds of dogs more than others, yellow labs hips wear out after a decade. These breeds have been bottlenecked by humans. Dogs can still breed with other dogs and when breeds mix often the resulting dog is stronger than either parent.
Of course I have been skirting the most important bottleneck in human history, Humans. I theorize, that humanity played on the shores of east Africa, eating fish and clams, urchins and tidal flat food. Due to the Laurentian Glacial mass, the sea levels were much lower, down about 100m. Not all the species were playing on the tidal flats. Some were wanderers and most likely, after looking at human history, ostracized from human culture at the time and stayed away for fear, about ten thousand individuals. How do we know this number? About one hundred thousand years ago in Indonesia, a volcano erupted, mount Toba. Volcanoes erupt all the time in Indonesia, but this eruption was very big; the caldera left after the eruption is over one hundred kilometers across.
The 2004 tsunami in the Indian Ocean, started in Indonesia as well. It devastated the coasts of India, Indonesia, Thailand, and many other nations including East Africa. East Africa, the tsunami was only a meter high, but it was still there. The mount Toba eruption, would have caused a Tsunami, much larger than the one in 2004. The wave would have been large enough to wipe the sea shore dwelling human off the map, leaving the disenchanted and ostracized, as the remains of the human species.
The bottleneck is bigger than that though, most humans would have remained in Africa, inheriting the vacated sea shores and spreading gradually up and down the coast. Only a few hundred of those left would have roamed their way out of Africa. And we know this because every human not native in history to Africa, has 5% Neanderthal DNA. And this was tracked down to about seven matings. Everyone from Europe, Asia, Americas, and Australia and the islands, has 5% Neanderthal DNA. Not in Africa. The people of the Philippines have 7% of another human subspecies and likely the other recent human subspecies found in Indonesia, probably added its DNA to the human mix.
Humans likely had familiar matings in the beginning but quickly stopped. Some cultures allow marriage between first cousins but the practice is rare and for good reasons, the European aristocracy discovered the problems; it concentrates bad genes as well as the good.
The proof? A study of mitochondrial DNA, passed to everyone from their mothers only showed that mutation rate of mitochondria and the variation of the DNA, that the divergence occurred about one hundred thousand years ago and from about ten thousand individuals. The Toba eruption caused global environmental change that lasted thousands of years, ash enveloped the world. Similar, albeit smaller, eruptions created tsunamis, based on the size and the place, it would have been huge, but there is no visual proof. That is because the area affected is under the oceans. Everyone forgets that in a world system, everything has an impact on everything else the ice age ended between 12,000bp and 6000bp and all evidence of human settlements from before this time, in their preferred habitat, on coasts on rivers would have been covered.
Bottlenecks affect our society and our entire species, the most genetically diverse people on this planet, are Africans and everyone else are from a handful of a handful of people.
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