What is the methodogy used to determine the exact genetic flow from one area to another and the times in which it flowed? [closed]

Question

For example, I take the instance of Central Asian migration into India.

Say geneticists studied a) ancient bones in CA b) ancient bones in India c) living people in Central Asia d) living people in India.

Case 1: -

Say they found a particular haplogroup (A) which is present only in Central Asians, and another one B, which is present in Indians (both living people, aka options c and d). Then they also found another haplogroup C, which is present in both individuals.

Question 1: - How do they then determine that it was the Central Asians who migrated and not Indians? Is it due to coupling this evidence with other sorts of evidence like general climate/vegetation? Or is it due to the fact that progressively, unique genes found in Central Asians decline in quantity when moving north to south, and the unique Indian genes aren't found outside India at all (Indus Valley genes)? And if I am not wrong, Indus Valley civilization people were descended from Africans who migrated via Yemen/Oman and the historical Elamites were their cousins, so even the so-called unique Indian gene can be found outside India...how do they then describe the direction of the gene flow?

Case 2:- Say the ancient bones of Central Asia (dated to 3000 BC) showed some genes which were common between ancient bones found in India (dated to 1500 BC).

Question 2: - Does this lead to the conclusion that the migration was from CA to India, latest by 1600-1500 BC? Is there any other technique to find the timing of the gene flow?

Question 3: - Modern ancestry tests have several obscure ancient groups like Neolithic Iranian farmers, Oriental Hunter-Gatherers, BMAC etc. Are all of these from bones taken in specific areas like Zagros Mountains (for iranic hg), Central Asia and Bactria (Afghanistan)? And these bones were dated to the specific time periods when these proposed civilizations were also historically dated?

Overall, I want to understand the nuance of the genetic tests which offhandedly say, that xyz group migrated to pqr location at abc era without giving the details.

Answer 1

Having just read A Short History of Humanity by Krause and Trappe, the argument seems to be as follows:

You calculate a "distance" (i.e. probably some useful metric) between the genomes e.g. of individual ancient and modern Central Asians and individusl ancient and modern Indians. Then there is probably some aggregation (clustering/averaging?). If the distance between ancient Central Asians and ancient Indians is considerably greater than between ancient Central Asians and modern Indians, the conclusion is that modern Indians have a considerable amount of (ancient) Central Asian ancestors.

You can do this if you assume that there is a constant mutation rate and that a great part of the human genome does not yield any evolutionary advantage and is only random noise (the authors claim that 50% of the human genome is just useless noise)

The authors of the book mentioned above are mainly dealing with Europe and are applying this argument not only to "ancient" remains and modern humans, but to remains from different ages. E.g. it seems to make quite a difference if your ancient Western European remains are 10000 or 6000 or 3500 years old.

Re. your question 2: The book notes that there is a considerable genetic difference between European human remains that are older respectively younger than roughly 4800 years. They conclude that this is because of a major migration wave from Eastern Europe (apparently the difference between older Eastern European remains and younger Western European remains is smaller). They note this fits well with various archeological evidence. I think the argument for migration into India could look similar.