I make a bottom-up reconstruction of the historical phonology and a portion of the lexicon of the Rote-Meto languages of western Timor. The regular sound correspondences of these languages necessitate reconstruction to Proto-Rote-Meto of a large amount of material that cannot be fully explained by Austronesian inheritance. The nature of this material indicates that it is substrate retention from pre-Austronesian languages of the region. This substrate can be detected by application of the comparative method alone. The bottom-up reconstruction also provides evidence for subgrouping Meto with both West Rote and East Rote and I propose that this is because Meto has shared a period of common development with both groups that involves a synthesis of the tree model and wave model of historical linguistics.