I've only read the abstract on this but (FWIW) Neves doesn't seem to be making a logical argument. He's claiming that because the morphology of ancient Indians is different than that of present Indians that therefore they descend from different populations. However this description proves the fallacy of that assumption.
"These earliest South Americans tend to be more similar to present-day Australians, Melanesians and sub-Saharan Africans,"
Australians (Aborigines) and sub-Saharan Africans are morphologically similar and genetically dissimilar. In fact they are so genetically dissimilar there are no human groups less related to each other.
"Australians (Aborigines) and sub-Saharan Africans are morphologically similar and genetically dissimilar. In fact they are so genetically dissimilar there are no human groups less related to each other. I agree. Everyone outside Sub-Saharan Africa are closer related than to anyone presently in Sub-Saharan Africa. In fact, the 'out-of-Africa' line that (suposedly) produced all of us, went extinct in Africa thousands of years ago.
Neves is pretty good so, I expect this is a translation or writers error.
Oppenheimer says the Orang Alsi (Malaysia) have the oldest DNA on earth.