What’s been going on? – Part 1: Why did the chicken cross the Pacific?

By Vicki Thomson

In the quest to find out what on earth is going on, I have been asking some animals how all the people of different cultures came together to create the modern world.

At home in New Zealand, I describe myself as a Pakeha, it means a New Zealander (Kiwi) of European descent. However, I also have some Maori blood. This means my ancestors were individuals of different cultures and homelands who all undertook travels to new worlds, and as a kid the stories behind these human journeys fascinated me. This interest led to degrees in Archaeology and, once I discovered the field of ancient DNA, Biochemistry. During my PhD, studying Australian biodiversity using modern and ancient DNA, I reinvigorated my interest in these childhood questions – I now use ancient DNA from archaeological remains of animals to track human migration! This post is part one of two on the origins of commensal and domesticated species in the Pacific and Island Southeast Asia (ISEA) – species introduced by the ancestors of my ancestors!

[Commensal species benefit from living in association with humans but where humans do not benefit nor are harmed by the relationship (e.g. rats). Domesticated species, on the other hand, are where humans modify the physical traits to give us some benefit (e.g. selective breeding of chickens for meat and egg production)]

Early Polynesians took pigs, dogs, rats, chickens, sweet potatoes, and bottle gourds as food items on their canoe voyages out into the Pacific – we assume they were uncertain of the
food resources that would be available during or at their journey’s end. Of these species, the chicken is the most useful for reconstructing the patterns of Polynesian migration routes as it contains relatively high levels of diversity and has a range of archaeological material available across the Pacific and ISEA. The origins of early Polynesians have been debated for the
last couple of hundred years, and it is still largely up in the air. So, what can a study of only a short fragment of the mitochondrial control region (mtDNA CR) from ancient chickens tell us?

[The mitochondrion is the site of energy release in the cell, there are many per cell, each with its own relatively small genome. The control region is a stretch of the mitochondrial DNA that does not encode any genes and so mutations are not under the control of selection (i.e. the mtDNA CR is very variable because it can mutate at will). There are 13 mtDNA CR haplogroups (groups of slightly different sequences with a defining trait, showing they came from a common ancestor) in chickens, each with slightly different evolutionary histories.]

Firstly, we needed to understand the diversity of chicken mitochondrial DNA around the world today. Some are widespread around the world due to European colonization in the last couple hundred years (e.g. haplogroup A, B, and E), but others are remarkably restricted to certain regions in Southeast Asia (e.g. haplogroup D).

We re-analyzed a handful of ancient Rapa Nui (Easter Island) chicken bones where a previous study had classified one as haplogroup E, linking it to an ancient chicken bone in South America, but when we looked at the same Rapa Nui bone we found it actually contained haplogroup D. So too did ancient chicken bones from Hawaii and Niue. When we looked at modern chickens in the Marquesas, Vanuatu, the Solomon Islands (including the Santa Cruz Islands), and islands in New Guinea, Indonesia, and the Philippines, a high proportion belonged to haplogroup D.

Above: Map showing the Pacific islands mentioned in the article: Western Polynesia is represented by the circle and Eastern Polynesia by the large triangle. Credit: V. Thomson

Now, you might think a continued high level of modern haplogroup D chickens is unlikely given the large amount of European activity in the Pacific since the 17^th century. But, if we think about the early peoples of ISEA and the Pacific, and the material culture/traditions they would have prized, then it may not be surprising that haplogroup D chickens are still common. Many Polynesian societies traditionally supported cockfighting (called ‘faatitoraamoa’ in Tahitian). Tahitians, specifically, had many songs and religious traditions (including ‘Ruaifaatoa’, the god of cockfighting) connected to faatitoraamoa, and it is possible that by transferring these traditions between island groups that cultural links were formed that would have provided support during bad times (e.g. poor harvests, cyclones, ecological devastation). These traditions may have been so entrenched that they prevented later European chickens being introduced more widely.

Getting back to the mismatch in results from the Rapa Nui chicken bone, we suggest that the reason this sample was initially thought to be haplogroup E, is due to one of the vagaries of ancient DNA: any modern DNA that might be contaminating laboratory reagents/equipment will outcompete the highly damaged DNA remaining in the animal after death. We were able to remove any potential modern DNA contaminating our study by using an enzyme to chew up modern DNA prior to adding the ancient DNA. This enzyme (shrimp DNase) has proven handy in all our lab’s studies on domesticate or commensal species, as we still live with chickens, rats, dogs, cows, etc. making it more likely their DNA will find its way into the labs and factories that produce the labware and reagents we use.

In addition to resolving this contamination issue, we also identified a unique signature present in all the ancient Polynesian chickens. Within haplogroup D there is a combination of four specific points in the DNA that vary only in the Polynesian chickens. We used this to reconstruct links between the ancient Polynesian chickens and modern chicken populations in the region, providing some clues as to the homeland of the Polynesian chicken. We found two samples in the Philippines that also had the four variable sites characteristic of the Polynesian chicken. We had hoped to find inklings of an origin for the unique Polynesian signature, and what we found suggests the Philippines is the place to focus our sampling efforts more intensively. Perhaps this is where my ancestors’ ancestors started the humble chicken on its Pacific journey.

UP NEXT…

A Pacific rat homeland in Island Southeast Asia

For the PNAS paper, see here

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