Recently (a few months ago) the Jomon have been shown to have carried not only Neanderthal DNA, but also Denisovan DNA. This evidences their ties with Melanesians/Papuans.
http://www.saitou-naruya-laboratory.org/assets/files/Seminar-Saitou-03-10-14.pdf
The study by Jinam et al. (2012) was shared by Dienekes on his blog when it was published, but it was behind a paywall. I have found it for free here:
http://www.saitou-naruya-laboratory.org/assets/files/pdf/J_Hum_Genet_57-787_2012.pdf
The study shows that Ainu are related to Sahulians (Papuans/Australian Aborigines). The level of Ainu admixture in ethnic Japanese highlighted by this study is consistent with higher Papuan+Melanesian admixture detected by others among Japanese than among other East Asians (http://oi57.tinypic.com/34ga841.jpg)
http://www.saitou-naruya-laboratory.org/assets/files/Seminar-Saitou-03-10-14.pdf
The study by Jinam et al. (2012) was shared by Dienekes on his blog when it was published, but it was behind a paywall. I have found it for free here:
http://www.saitou-naruya-laboratory.org/assets/files/pdf/J_Hum_Genet_57-787_2012.pdf
The study shows that Ainu are related to Sahulians (Papuans/Australian Aborigines). The level of Ainu admixture in ethnic Japanese highlighted by this study is consistent with higher Papuan+Melanesian admixture detected by others among Japanese than among other East Asians (http://oi57.tinypic.com/34ga841.jpg)