Applying Shotgun Proteomics to Understand Interactions among Humans and Suid Species in Island Southeast Asia and the Pacific

Sofia Samper Carro1*, Philip Piper2, Andi Muhammad Saiful3, Budianto Hakim4, and Adam Brumm5

Pigs, as important economic and symbolic assets in Island Southeast Asia (ISEA) communities, have been proposed as one of the main resources introduced by Neolithic farmers - and pigs, along with chickens were certainly the first domestic animals to reach Near Oceania. Genetic evidence on Asian modern suids indicates that pigs were likely translocated from the mainland across ISEA and out into the Pacific. Although it is relatively straightforward to identify pig introductions on islands that were devoid of native/endemic species, it has proven much more difficult to identify the arrival of domestic pigs on islands where endemic pig species were present before human arrival. Hence the status of some early records of pig introductions in ISEA is difficult to confirm, due to limited means of differentiating the bones of domestic pigs from wild boar or endemic species. The application of paleoproteomics to investigate pig domestication history in the Indo-Pacific provides an alternative technique to analyse and identify samples from archaeological sites in the region. Here we present the first collagen and non-collagen protein sequences assembled for two key species in the region: Babyrousa celebensis and Sus celebensis. Through a combination of manual and automated collagen extraction protocols and label-free quantification, we conducted a blind test on modern specimens to determine whether shotgun proteomics is a valid technique for distinguishing between these suid species. Predicted sequences were further tested on significant archaeological material from Timor-Leste, Sulawesi and Pacific Islands to evaluate the taxonomic resolution of our results.