Mitochondrial genome reconstruction of Rattus rattus obtained from an owl pellet from Tres Bocas Cave in the Dominican Republics

Abstract

Molecules of DNA are ubiquitous in the environment and a rich source of biological information, but because DNA degrades rapidly in tropical climates studies of ancient DNA in the Caribbean have been limited until recently. Fossilized owl pellets are one potential source of ancient DNA with useful phylogenetic information. In this study, we obtained a fossilized Rattus rattus sample from an owl pellet excavated from Tres Bocas Cave in the Dominican Republic. We sequenced DNA pooled from three rat maxillae from the pellet, annotated the mitochondrial genome and compared the sequence to contemporary data from R. rattus from other studies. Maximum Likelihood phylogenetic analysis showed the sample from the Dominican Republic was nested within a clade of R. rattus from Madagascar and East Africa. The sequence from R. rattus from the Dominican Republic had few nucleotide misincorporations, suggesting a recent origin, which was corroborated with 14C isotope ratios that indicated the sample dates from 1960-70. We have demonstrated that phylogenetic information can be obtained from DNA from bones in decades-old pellets in a tropical region, which validates an ancient DNA extraction technique and indicates further sampling in the Caribbean may prove fruitful.