The feathers of tropical birds were one of the most significant symbols of economic, social, and political status in the pre-Columbian Americas. In the Andes, finely produced clothing and textiles containing multicolored feathers of tropical parrots materialized power, prestige, distinction, and were particularly appreciated by political and religious elites. Here, we report 27 complete or partial remains of macaws and amazon parrots from five archaeological sites in the Atacama Desert of northern Chile to improve our understanding of their taxonomic identity, chronology, cultural context, and mechanisms of acquisition. We conducted a mutiproxy archaeometric study that included zooarchaeological analysis, carbon and nitrogen stable isotopic dietary reconstruction, AMS radiocarbon dating, and paleogenomic analysis. The results reveal that during the Late Intermediate Period (1150-1450 CE) people in this region acquired Scarlet Macaws (Ara macao) and at least five additional tropical parrot species through vast exchange networks that extended over 500 km towards the Amazonian tropical lowlands. Stable isotopes indicate that Atacama aviculturalists sustained these birds on diets rich in marine-bird-guano-fertilized maize-based foods. The captive rearing of these colorful, exotic, and charismatic birds served to unambiguously signal relational wealth in a context of emergent intercommunity competition.

Ancient DNA was extracted from scarlet macaws recovered from the Atacama Desert.

Using the DNA extraction and isolation protocols detailed in George, et al. (28) ten samples were processed at the Pennsylvania State University Ancient DNA Laboratory and summarized below. Bone and feather samples were treated with a mild 1% bleach solution followed by multiple water washes to remove surface contamination. Bone surfaces were removed and homogenized into a fine powder using a mikro-dismembrator (Sartorius) ball mill with tungsten carbide balls. Approximately 75-100 mg of bone powder was processed following the DNA extraction and purification protocols described in Dabney, et al. (29) with modifications described in George, et al. (28). Feather DNA extractions used ~20-30 mg of the calamus, sliced into ~1 mm pieces to expose a larger surface area in the extraction buffer. The following extraction buffer modifications were made for keratinous tissues: 0.45m EDTA, 0.5% N-lauroylsarcosine, 50 mM DTT, and 0.25 mg/ml proteinase K, incubated with rotation for 24 hours at 45 °C. The calamus DNA extracts were purified and processed followed the same workflow as above.

DNA sequencing libraries were constructed, indexed, and amplified at the Smithsonian Institution’s Museum Support Center, Washington, D.C. DNA extracts and DNA libraries were quantified using Qubit ® (Life Technologies) fluorometer. Illumina-specific barcoded adapters were prepared using DNA extract input volumes of 25 µL following the “BEST” protocol (30). Library amplification and post-PCR procedures followed the dual-index approach (31) with modifications and purification steps described in Kennett, et al. (6). Amplified DNA libraries were enriched for mitochondrial DNA fragments using bead capture in-solution biotinylated RNA bait hybridization (32) at the PSU Department of Anthropology. Custom capture probe sets by MyCroarray, Inc. (probe design: 140429 and 150610) were designed using a complete Ara macao mitochondrial input reference sequence (GenBank accession number: CM002021.1; (33)) with 100-mer probes that were tiled every 10 base pairs (bp). All in-solution hybridization enrichment and post-capture amplification followed the manufacturer’s protocol (version 4.01). Post-capture DNA libraries were pooled in equimolar ratios and sequenced at the NYU Medical Center on an Illumina NextSeq® 500 High Output Kit v2 (75 cycles, 400 MM reads max).

Sequenced reads were de-multiplexed following standard procedures at the NYU Medical Center. Prior to assembly, raw reads were trimmed for adapters and low-quality stretches of ambiguous bases at the 5’/3’ termini using AdapterRemoval 2.1.7 (34). Merged reads were mapped to the revised Ara macao reference mitogenome sequence (28, 33) using the BWA-backtrack algorithm in the Burrow-Wheeler Aligner following parameter -l 16500 v. 0.7.5 (35). All duplicate and read removal (<30bp), filtering (<q30,), and masking was completed using SAMtools-0.1.19 (36). An assessment of ancient endogenous macaw mtDNA read authenticity was completed using MapDamage 2.0 (37) and PMDtools (38) and hard-masked the average overhanging bias per samples to limit errors in the alignment due to damaged derived errors (6). Consensus sequences were generated using a custom Perl script that enforced a minimum of 2x non-redundant coverage and 80% site identity and visual examined for alignment errors using Geneious version 2020.1.2.