Identifying Complex DNA Contamination in Pig-Footed Bandicoots Helps to Clarify an Anomalous Ecological Transition

Abstract

Our understanding of the biology of the extinct pig-footed bandicoots (Chaeropus) has been substantially revised over the past two decades by both molecular and morphological research. Resolving the systematic and temporal contexts of Chaeropus evolution has relied heavily on sequencing DNA from century-old specimens. We have used sliding window BLASTs and phylogeny reconstruction, as well as cumulative likelihood and apomorphy distributions, to identify contamination in sequences from both species of pig-footed bandicoot. The sources of non-target DNA that were identified range from other bandicoot species to a bird—emphasizing the importance of sequence authentication for historical museum specimens, as has become standard for ancient DNA studies. Upon excluding the putatively contaminated fragments, Chaeropus was resolved as the sister to all other bandicoots (Peramelidae), to the exclusion of bilbies (Macrotis). The estimated divergence time between the two Chaeropus species also decreases in better agreement with the fossil record. This study provides evolutionary context for testing hypotheses on the ecological transition of pig-footed bandicoots from semi-fossorial omnivores towards cursorial grazers, which in turn may represent the only breach of deeply conserved ecospace partitioning between modern Australo-Papuan marsupial orders.