Just realized. The Science paper has some interesting dates which allows us to make the above inference.
- Separation between Europeans and East Asians 25-38 thousand years before present.
- Gene flow between proto-East Asians and proto-Australians before the Native Americans diverged from the former 15 thousand years before the present.
- A conservative first landing in Australia 40-45 thousand years before the present.
The Native American result, where they share some derived variants unique to East Eurasians (mutations which emerged after the separation from West Eurasians) with Aborigines, pegs a minimum date of admixture ~15,000 years ago. But, obviously the admixture had to occur after the divergence of West and East Eurasians. Let’s say ~30,000 years ago. Even assuming that the gene flow between East Eurasians and proto-Australians occurred immediately after the separation 38,000 ago, there were anatomically modern humans in Australia for thousands of years already! The implication is that the first Australians by necessity can not have contributed in totality the ancestry of modern Aborigines. The AJHG paper gives a 50:50 estimate for the ratio of proto-Australian and the Andaman Islander/Malaysian-Negrito related population. We don’t need to be certain of the exact value to assume that numbers like this imply considerable admixture above trace levels.
Of all the dates I’m probably most confident about the archaeological ones about the settlement of Australia by anatomically modern humans. 46,000 years ago the megafauna started going extinct. That’s an immediate tell that humans have been let into the garden.