The article says that all human Y-chromosome can be calculated to have to come from one Y-chromosome a long time ago. It doesn't mean that there was
no Y-chromosome before that. It doesn't even mean that there was only one at that time, only that we descended from one of the large group. But it's
just a calculation with the current differences in the Y-chromosome, so it doesn't even has to be true.
This was actually already discovered in 1996. The article is called "Absence of Polymorphism at the ZFY locus on
the Human Y Chromosome", Science, May 26, 1995, p. 1184ff. A summary can be found
here.
If I'm correct, almost all mammals have Y-chromosomes. Some of you here interpreted the article so that humans at one point didn't have a
Y-chromosome. Why would humans, who evolved from mammals, lose their Y-chromosomes only to get them back later?