The Rise and Fall of the Passenger Pigeon

Reconstruction of past environments typically requires an a priori assumption of ‘what could have been present’ through the use of reference data sets. In the case of ancient DNA approaches such reference sets stretch to the thousands of organisms. Since the number of species is actually much higher many species will not be represented. Consequently, phylogenetic assignation will tend to assign the ‘closest’ organism as the true organism of origin. This will lead to the assignment of ancient DNA to model organisms, and organisms that make little geographic sense. Such assignations are often removed as ‘contamination’, thereby introducing inferences that are not derived from the data itself but a perception of expectation of the environment from other information sources. However, this tendency becomes very problematic if the organisms that are of interest also happen to be model organisms, such as the flora and fauna that characterize the Neolithic. We applied a novel palaeometagenomic approach to be more robust to partial representation of organisms in the database so that no a priori assumptions had to be applied to the data and all inference was derived from the genetic data itself. The removal of the restriction of high database coverage allowed us to move outside of typical barcoding areas of the genome and increase our sensitivity of organism detection. The result was that we were able to reconstruct an early Neolithic environment that changes our understanding of the Neolithisation of Northern Europe.