Archaeogenomic evidence from the Southwestern US points to a Pre-Hispanic scarlet macaw breeding colony

We sequenced ancient mitogenomes from the bones of 17 scarlet macaws excavated from two sites in Chaco Canyon (n=13 macaws), three sites in the Mimbres region (n=3 macaws), and to add some spatial and temporal variation, one site (ArroyoHondo; n=1 macaw) in north central New Mexico. We preparedmassively parallel sequencing libraries from each extract, but prior to sequencingwe used a DNA capture approach to enrich our libraries for scarlet macawmitochondrial DNA fragments, using biotinylated RNA baits complementary tothe reference scarlet macaw mitochondrial genome sequence. Post-capture libraries were then sequenced using the Illumina HiSeq 2500 and Illumina NextSeq 500 platforms. Only one mitochondrial DNA haplogroup is present of the five historically known haplogroups in the lowland forests of Mexico and Central America. Phylogenetic analyses indicate the ancient macaw lineage in the SW shared genetic affinities with this wild lineage. These data support the hypothesis that a translocated breeding colonyof scarlet macaws existed some distance north of their endemic range, and birdswere acquired from this unknown location for nearly three centuries.