[HuShifang]

The Yamato ethnicity (大和民族 Yamato minzoku), primarily descended from the Yayoi people (who are relatively recent arrivals from the mainland, i.e. first millennium CE), historically occupied Honshu, Kyushu, and Shikoku. They're the ethnic group usually called "Japanese," and the majority. The Ainu ethnicity, primarily descended from the Jomon people (who represented an earlier wave of in-migration to the Japanese archipelago, thousands of years BCE), historically occupied Hokkaido. Hokkaido was only integrated into the main Japanese polity in the last few hundred years.

But, it's all fraught and complicated, conceptually(/politically/culturally) and empirically. (For instance, Yamato people also have Jomon heritage, and these days most Ainu also have Yayoi / Yamato heritage.) So indeed, indigeneity is complicated here, just like it is, as you say, everywhere.

[Mediterraneo10]

There were known Ainu populations in northern Honshu as well before the Yamato fully assimilated them, though this process happened centuries ago. The Ainu were not limited to Hokkaido.

[HuShifang]

Yup -- I just didn't want to go into too much detail.

David Howell at Harvard has written quite a bit about identity in Japan -- see esp. "Geographies of Identity in Nineteenth-Century Japan" (2005).

[state]

Any other recommendations in the category of long-term Japanese history and anthropology? I find this subject really interesting, but have struggled to find good sources.

[HuShifang]

Honestly, I'm much more familiar with China scholarship than Japan scholarship, and with historical scholarship than anthropological. But Bruce Batten's To the Ends of Japan might be worth a read. There are also quite a few scholarly works concerning the role of kokugaku (roughly, "national learning") -- a fairly fundamentalist, xenophobic school of philology and philosophy that sought to purge Japanese culture of foreign "impurities", and rose to prominence from the Meiji Restoration through WWII. (It also exercised considerable influence on modern Japanese archaeology in its formative period; my impression is that its nativist premises colored many early archaeologists' findings.) Stuff on social status (John Hall's "container society" and more recent materials) might be interesting too -- e.g. on the status of burakumin).