Pottery residues provide earliest direct evidence for domestication and dairy processing in equatorial Mainland Southeast Asia

The advent of Neolithic farming and domestication in the Yangtze Basin in Southern China triggered the rapid dispersal of farming societies across Mainland Southeast Asia (MSEA) throughout the mid-late Holocene. The impact of this expansion on the local consumption economy of Neolithic communities in the equatorial zone of MSEA (Southern Thailand and Peninsular Malaysia), however, remains unclear in the archaeological record to date, primarily due to the absence of reliable zoological and archaeobotanical evidence. Here, we apply a simultaneous multi-omics approach to retrieve ancient proteins, lipids and metabolites from Neolithic ceramic sherds recovered from three archaeological sites in Peninsular Malaysia. Our study reveals the earliest direct evidence for the appearance of domestication and dairying in this region by 3,000 years BP (Before Present). Our results offer new insights into early Neolithic animal domestication and plant use in the equatorial zone of MSEA undocumented in the archaeological record until now, while lending support to zooarchaeological and stable isotope studies.