DOI: 10.25349/d95c99
title: Precolumbian Transregional Captive Rearing of Amazonian Parrots in the Atacama Desert

description: 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.
description: Ancient DNA was extracted from scarlet macaws recovered from the
 Atacama Desert. Using the DNA extraction and
 isolation protocols detailed in George<i>, et al.</i> (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<i>, et al.</i> (29) with modifications described in
 George<i>, et al.</i> (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<i>, et
 al.</i> (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 <i>Ara macao</i> 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
 <i>Ara macao</i> 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
 (&lt;30bp), filtering (&lt;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.