They can't distinguish at this point. I wonder if examining the Y DNA and mitochondrial DNA patterns of the same populations might shed light on the gender breakdown of the genes, which might be something that can be correlated with patterns of gender representation in migrations.
Interesting paper, but it seems to suggest that all the Native American Y-DNA on Rapa Nui is explainable by the 19th century Peruvian slave trade, not contact between Polynesians and South Americans centuries earlier.