This is a really interesting subject with so many possible theses.
To state the obvious, we are all intellectually very different. And I don’t think the difference between now and 40,000 years ago has to be all that significant. The less intelligent half of the population is fully human, obviously, but if everybody were at that level of intelligence, we would quite clearly still be making simple stone tools and living in caves. The difference between now and 40,000 years ago is therefore less than the natural variation in the population we see today. So I don’t think the question of the psychological unity of mankind is really answered by considering selection over the last 40,000 or so years.
This isn’t to say there might not be some quite significant changes in the population—even over historic time. If significant changes can happen in the way we digest milk in the time between now and the Romans, it’s possible that average psychology has changed too. Our psychological environment has certainly been different over that period from our stone age forbears. Are we less aggressive? Brighter? On average, I mean.
One more thought. The average sweeping change in our genome, the author says, is about 5500 years old. This figure is almost certainly wrong, as it has a visibility bias. Mutations from that long ago have had time to become numerous, and so we have discovered them. But there must be many more such changes that one would have expected to have arisen in the far more numerous modern populations. These mutations probably exist in only tens, hundreds or thousands of people at the moment, and have therefore not been discovered. But if they have a selective advantage, they will grow. Assuming population genetics as usual, in 5500 years, there will be perhaps 10, 20, 50 times as many genes obviously sweeping the population as are obvious today.
For me the primary evidence of a bunk claim is when the claimant fails to reasonably deal with the mainstream. Let’s take the creation evolution debate. If someone comes along claiming a creationist position, but is completely unable to even describe what the evolutionary position is, or what might be good about it, then their idea is bunk. If someone is very good at explaining evolution as it really happens, but then goes on to claim something different can happen as well—then it becomes interesting.
Anyone proposing an alternative idea needs to know precisely what it is an alternative to—otherwise they haven’t done their homework, and it isn’t worth my time.