Chickens in the Americas: the Spanish introduction, and the one bone that disputes it
Eighty-four per cent of native chickens sampled across mainland South America carry mitochondrial haplogroup E, the lineage that dominates Europe, and the Pacific lineage is absent from the continent altogether - which makes the Iberian introduction of the sixteenth century the measurable origin of the American farmyard bird. One directly dated bone from Arauco in Chile has been argued since 2007 to be older than that, and the argument is still running in print.
Why this wins its question: Coverage of this question is split between two incompatible headlines that each cite one paper: popular accounts either report that Polynesians brought chickens to Chile before Columbus, resting on the 2007 PNAS paper alone, or state flatly that the Spanish introduced the chicken with no evidence attached at all. Neither side prints the numbers, and almost nobody notes that the argument continued through a 2008 rebuttal, a 2014 ancient-DNA study, three dissenting letters and a reply in the same journal, and a 2020 continental survey. This object assembles the whole sequence in date order with the measured quantities in the text - 229 birds sampled, haplogroup E at 83.96%, haplogroup D absent from the mainland, one bone at 622 +/- 35 B.P. from a site three kilometres from the sea and never corrected for marine carbon - and it keeps the losing side registered and quoted rather than deleted, because the dispute is about evidence and the reader is entitled to see what the evidence is. It also draws the line the 2020 authors themselves draw: this settles the ancestry of living South American chickens, not the question of whether Polynesians reached the continent.
Claims
Every assertion below is bound to registered sources and carries its own confidence. Weight them; do not treat the page as uniformly authoritative.
The modern evidence for a European origin is a frequency, not an inference. A 2020 survey sequenced the mitochondrial control region of 229 native chickens from Brazil, Chile, Colombia and Peru against a worldwide comparative set and found that "Haplogroup E is the most predominant mitochondrial CR region lineage observed in South America comprising 83.96% of all chickens on the continent", with haplogroups A at 7.35%, B at 4.68% and C at 4.00%. The authors' reading is explicit: "Given the high frequency of this haplogroup in Europe along with the historical records and observations that Spanish and Portuguese brought chickens to the Americas, Europe may be the more likely source of modern chickens in South America."
The negative result in the same study is the sharper one, because it is what an alternative introduction would have had to leave behind. Haplogroup D - the lineage ubiquitous in island Southeast Asia and across the Pacific islands - "has not been found in modern South American chickens in this study". Whatever else reached the continent, the Iberian stock is what the farmyard population descends from.
The claim that disputes this is precise and small: a single chicken bone from El Arenal-1 on the Arauco Peninsula in south-central Chile, one of fifty chicken bones from the site representing a minimum of five birds. Directly dated in 2007 at "622 +/- 35 B.P., resulting in a calibrated age range of AD 1321-1407", and at two sigma AD 1304-1424, it would be pre-Columbian; its mitochondrial sequence was reported identical to ancient chicken bones from Tonga and American Samoa, which the authors read as a Polynesian introduction. Their case rested partly on a historical difficulty they state plainly - that Pizarro in 1532 found chickens already integral to Inca economy and culture, which would require very rapid dispersal from an Atlantic landfall around 1500.
The rebuttal came the following year and attacked both halves. On the DNA, the El Arenal sequence falls in haplotype 8, the single most common chicken haplotype in the world and one indistinguishable from European and South Asian birds, so that "the position of the single Chilean pre-Columbian chicken sequence within the worldwide distributed haplotype 8 removes any genetic support for a Polynesian introduction of this haplotype to South America". On the date, the site lies under three kilometres from the ocean and the sample was not corrected for marine carbon; the same authors note that the dating laboratory used "has recently been suggested to have overestimated the age of zooarchaeological bones elsewhere in the Pacific". The marine-offset argument is modelling rather than measurement - no isotope data were reported - which is why this claim is not carried higher.
The same 2008 study is where the Spanish introduction is stated as a positive finding rather than a default: analysing modern Chilean birds, the authors "consider the clustering of the modern Chilean chicken sequences with haplotypes predominant in Europe to indicate the contribution of Spanish introduced chickens". It is worth noting what this does and does not settle - it identifies the ancestry of the living population, not the first arrival of the species.
A larger ancient-DNA study in 2014 defined what a genuine Polynesian signature looks like and then looked for it in the Americas. Sequencing archaeological chicken bones across the Pacific, it identified a cluster of haplogroup D sequences "defined by a diagnostic combination of four CR SNPs (which we term the 'ancestral Polynesian motif')" as the founding lineages carried across the Pacific, and concluded that "no early South American chicken samples have been detected with the diagnostic Polynesian mtDNA haplotypes, arguing against reports that chickens provide evidence of Polynesian contact with pre-European South America". The 2007 result was attributed to contamination of ancient samples with modern chicken DNA.
The dispute did not end there, and an honest object has to say so. The 2014 paper was answered in the same journal by three letters and a reply, printed at E3582 to E3585. The authors of the 2007 study argue in theirs that haplotype E was the first lineage carried into the Pacific, that "of the 15 E haplotypes identified in ancient Pacific chickens, 12 come from sites predating A.D. 1000, where no D haplotypes have been found", and that the contamination study cited against them actually reports one chicken contaminant in 779 no-template control reactions. This is an unrefereed letter by an interested party and is carried accordingly; it is registered here because a corpus that reports only the rebuttal would be reporting a closed question that is not closed.
The most recent of the studies registered here draws the boundary that this object adopts. Its authors state that their result is about descent, not about contact: "All we can say is that there is no evidence for Polynesian chicken genetic signatures being retained by contemporary South American chickens", which "does not discount the potential for a pre-Columbian introduction of chickens by the Polynesians to South America". Polynesian contact with the Americas is separately evidenced - the sweet potato is the standard case - so the chicken question is narrower than the contact question, and losing the first does not settle the second.
What the Spanish contribution here actually consists of, stated without inflation. The chicken is not native to the Americas and "has never been recovered or reported from paleontological, Paleo-Indian, or ... prehistoric archaeological contexts in the Americas" outside the disputed Chilean find; the Iberian voyages carried an Old World domesticate across, and four to five centuries later the maternal ancestry of the mainland farmyard population is still traceable to that transfer in 84% of sampled birds. That is a contribution of biological consequence and of no evident intention: no crown programme is involved, only ships provisioned with poultry.