We thank E.I. Rogaev for access to ancient DNA facility.
The Paleo-DNA Laboratory is a dedicated ancient DNA facility with stringent precautions and protocols employed for the analysis of degraded DNA.
Ultimately, all samples were either consistently negative or amplified at least twice, in both the UMSL laboratory and the ancient DNA facility.
In addition, a subset of four Huia samples were independently extracted and amplified for three loci (Pca01, Pca05, and Pca12) at an ancient DNA facility at the University of Auckland.
Three independent extracts of aurochs DNA from sample CPC98 (labelled C1, C2 and C3), each organised into three separate ∼30 µl aliquots (labelled C11 3, C21 3 and C31 3 —giving a total of nine aliquots), were prepared for high-throughput sequencing using an Illumina Genome Analyzer, in a dedicated ancient DNA facility based in the Smurfit Institute of Genetics, Trinity College Dublin.
DNA was extracted from five King Island Emu sub-fossil bones (Museum Victoria numbers B226 450 55, 55 and 57, KI01-04 in this study respectively, B226 43 was excluded from further analysis after molecular damage proved too excessive) together with a mock extraction in a dedicated ancient DNA facility at Griffith University, Nathan, Australia.
All extraction steps and PCR set up was done in a dedicated ancient DNA facility, away from any PCR or post-PCR areas.
In accordance with criteria suggested for the verification of aDNA sequences [ 47], a number of samples were extracted and sequenced at a separate ancient DNA facility at Massey University, Auckland, New Zealand.
DNA was extracted from blood, tissue, and feather samples using the DNeasy Tissue kit and manufacturer protocols (Qiagen, Inc .. Museum specimens were handled in a dedicated ancient DNA facility using a modified Qiagen DNeasy Tissue kit protocol [ 23].
