This field of study is so crowded with arcane terminology and forbidding jargon that Evanjehadi crooks like Tony Joseph are able to get away with claiming that all kinds of BS conclusions have been "scientifically proven".
I have attempted to write an explanation suited to the layperson, below.
To put it in a very simple analogy, think of this.
In India you find many people with a genetic marker called R1a-M417. Let’s visualize this variation as a big black dot on their foreheads.
Now there are some people in India who have genetic markers that define “sub-clades” of R1a-M417, with names such as Z94-Y40-Y37. Let us visualize these people as having the big black dot on their foreheads (the R1a-M417 marker), plus a little blue dot alongside the big black dot (the Z94-Y40-Y37 marker). So these people are a subset of all R1a-M417 (black dot carrying) people.
Genetics can tell you approximately how old these markers are. Let’s say genetics find out that the big black dot (R1a-M417) is a variation that developed in a common ancestor, a single individual who would be the great-great-great^300-grandfather of many Indians, Europeans, Central Asians etc. alive today.
Genetics can also tell that the little blue dot is more recent in appearance. It appears in a sub-fraction of people descended from that common great-great-great^300-grandfather (all the black-dot folks). This sub-fraction had a more recent common ancestor, say a great-great-great^175-grandfather who was the first black-dot-carrying individual in whom the variation of a little blue dot first appeared.
And that’s about all genetics can say.
The Silva et al paper observes that there are individuals in India (Z94-Y40-Y37) who have both black dots and blue dots on their foreheads. So they must have had this one common ancestor, the great-great-great^175-grandfather, who was obviously more recent than the great-great-great^300-grandfather (black-dot-only, the original bearer of the R1a-M417 variation, who lived about 6,000 years ago).
Silva et al make the following observations:
1) There are people all over Eurasia, Central Asia etc. in addition to India who have the black dot on their foreheads. All of them were descended from the individual we are calling great-great-great^300-grandfather (the original bearer of the R1a-M417 variation).
2) There are people specifically and only in India who have black and blue dots on their foreheads. All of them were descended from the individual we are calling great-great-great^175-grandfather (the original bearer of Z94-Y40-Y37 variation within R1a-M417).
3) Meanwhile there are people in other parts of the R1a-M417 territory who have other combinations of dots on their foreheads. Some may have black dot (R1a-M417) plus red dot (Z93-Z2122) in Eastern Europe. Others may have black dot (R1a-M417) plus green dot (Z94-Y40-Z667) in Arabia.
4) According to Silva’s results, genetic analysis suggests that the common ancestors of red+black dot and green+black dot (not present in India) are more ancient than the common ancestor of blue+black dot (present in India).
They use this to spin the following bogus conclusion:
Because non-Indian R1a-M417 subsets like red+black dot (Z93-Z2122) and green+black dot (Z94-Y40-Z667) are descended from common ancestors more ancient than many Indian R1a-M417 subsets like blue+black dot (Z94-Y40-Y37)… therefore, nobody with a black dot on his forehead (R1a-M417) ever lived in India before some TFTA Aryans, who were blue+black dot, brought the entire R1a khandaan into the Indian gene pool for the very first time about 3500 years ago.
To accept their conclusion, you also have to accept the completely unproven allegation that the individual we called "great-great-great^175-grandfather" (the first person ever to have the blue+black dot variation, or Z94-Y40-Y37 marker), must have been one of those Aryans who came from Central Asia to India 3500 years ago. You have to accept on faith, based on nothing but the incestuous race-theorizing of the AIT fraternity, that this man could not have been an Indian himself.
Visualized like this it is easy to see that this is utterly specious rubbish.
The basic assumption (i.e. nobody from the original black-dot khandaan ever lived in India until these Aryans came) is completely unsubstantiated. Indeed, Underhill and many others have demonstrated the possibility that R1a-M417 could have emerged from India itself.
The paper provides absolutely no reason why:
1) R1a-M417 could not have arisen in India 6000 years ago, and then spread out of India to Europe, Central Asia, Arabia, etc.
2) Variations like red+black dot (Z93-Z2122) and green+black dot (Z94-Y40-Z667) arose in those populations of R1a-M417 descendants who went out of India and lived in Europe, Arabia etc. but did not arise in India itself, the original home of R1a-M417.
3) At a later date, variations like blue+black dot (Z94-Y40-Y37) arose amongst a subset of the R1a-M417 descendants who remained in India.
It does not help Silva et al’s case that their specious conclusion… TFTA Aryans bringing R1a-M417 into the Indian gene pool… relies entirely on Y-chromosomal DNA, the kind that is only passed on from father to son, and has NO supporting evidence to be seen in either autosomal DNA or mitochondrial DNA (passed exclusively along the maternal line).
Forget Occam’s razor. Accepting Silva et al’s conclusions would require a razor that is too blunt to shave with.
Now Tony Joseph is a whole other can of worms unto himself. He has taken the bad science espoused by Silva and gang, and constructed an Evanjehadi edifice of deceit upon it, made up of disingenuous Marxist gibberish about Sanskrit, Rigveda and all kinds of things that no self-respecting geneticist would ever presume to demonstrate.