If you really think about it languages cannot be an isolate, that is, unless at the creation of the language it developed out of a population that had no language.
It is now accepted that about 70,000 years ago our species spread from Africa into Europe and Asia. As these populations migrated they some settled. It is possible language had yet developed, or least not fully. Nonetheless, there is a protolanguage that probably existed.
The influence of such a language, or influence of subsequent languages must exist. What is not noticed is that that influence remains within the language, much like how scholars noticed the similarities between Sanskrit and the languages of Europe.
And as much as people want to think of Japanese as a language isolate, people or peoples must have migrated from the main Asiatic continent. The idea of ‘peoples’ might explain the difficulty to trace a language like Japanese of its origin. Japan was a crossroad to the North American continent with routes from the south and the north as well as possible reverse migration from America as well.
Whatever the truth, it is now still possible to trace the genetic origins of people “fairly accurately”. And with genetics also comes influence of language, society, and culture.