I think the latest thinking is that all people of Japan to varying degrees are descended from the Jomon people along with other populations migrating from mainland Asia over millennia.
This pattern - early hunter gatherer populations forming the substratum that later mixed with larger migrations of agricultural populations - is not unique to Japan.
It's quite similar to what you find in the paleogenetics and history of most regions of the world, including Europe and South Asia.
My understanding of more recent European population studies is that the genetic signature of the pre-agrarian hunter gatherers is actually quite low. In general they were displaced rather than merged. Or their numbers were so low and diffuse that their contribution was little. Which makes sense when you consider population densities possible/typical in a hunter gatherer vs agrarian lifestyles.
We're back to population migration / replacement theories being ascendant rather than the situation 30 years ago when cultural diffusion theories were preferred.
10% of the average Briton's ancestry (for those without recently migrated ancestors) is attributable to West European Mesolithic hunter gathers. That's a pretty significant chunk, suggesting both migration and mixture happened, and not diffusion or replacement.
"When we look at genetic variation in modern British people today, we find that – for those who do not have a recent history of migration – around 10% of their ancestry can be attributed to the ancient European population to which Cheddar Man belonged. This group is referred to as the western European Mesolithic hunter-gatherers. However, this ancestry does not relate specifically to Cheddar Man or the Mesolithic population of Britain. Well after Cheddar Man’s death, two large-scale prehistoric migrations into Britain produced significant population turnovers13. Both of these migrations into Britain represented westward extensions of population movements across Europe10-12. In both cases, these migrating populations intermixed with local people who carried western European Mesolithic hunter-gatherer ancestry, as they moved across Europe. When these populations arrived in Britain they already had some hunter-gatherer ancestry derived from this mixing with local populations. Therefore the majority of western European Mesolithic hunter-gatherers ancestry that we see in modern British people probably originates from populations who lived all over Europe during the Mesolithic, which was carried into Britain by these later migrations."
