How many species that are extant today were around 5000 years ago?

Most species around 5000 years ago can be found alive today. Species that become extinct become extinct relatively quickly, so any extinctions that occurred 5000 years ago happened recently enough that they are still widely visible in the fossil record. Of course, 5000 years is long enough for changes in species distribution and other changes in ecology, but the broad outlines of the world's extant biodiversity have been in place for at least that long.