To this day there are many things we don’t know about how modern humans first reached and populated the Philippines. The latest scientific knowledge proposes that around 4,200 to 4,000 years before present, Austronesian-speaking people traveled south from Taiwan and eventually occupied the archipelago, most of Island Southeast Asia and beyond.
What we do know of that past, we owe in part to archaeologists and other scholars, who piece together a narrative of what transpired from physical traces people left behind. Moreover, modern humans definitely did not come alone, bringing with them domesticated animals like dogs, pigs, and chickens.
Knowing this, a team led by Dr. Michael James B. Herrera of the University of the Philippines Diliman School of Archaeology aimed to shed more light on how humans in the Sulu Archipelago might have lived, traveled, and interacted, by studying the genetic diversity of their chickens (Gallus gallus). Their Sept. 10, 2025 paper, published in Royal Society Open Science, studied these chickens’ mitochondrial DNA, looking into how their lineage and genetic diversity might hint at the migration patterns and activities of the people that lived alongside them.
The UP Diliman team was joined by scholars from Mindanao State University – Tawi-Tawi College of Technology and Oceanography, as well as the National Museum of Natural History. Photo from Michael James B. Herrera, UPD School of Archaeology.
When one looks at history and culture, the choice to study chickens makes sense. According to the paper, people in the Sulu Archipelago have and continue to show a deep dependence on chickens, and vice versa. This relationship, referred to as “entanglement” can be seen in the archipelago’s various chicken-based dishes, rituals, arts and ceremonies. This pattern is also seen in the closely-related people of Borneo and broader Indonesia.
The team began by extracting DNA from body feathers of 254 village chickens from 16 islands in the Sulu Archipelago and the Zamboanga peninsula. From these samples, they then amplified and assembled a control region made up of 764 DNA base pairs of mtDNA. These sequences were arranged according to their haplogroups, clusters that share the same ancient common ancestry based on unique patterns of genetic variation or haplotypes.
A total of 254 chickens across the Sulu Archipelago and the Zamboanga peninsula were sampled for mitochondrial DNA through their feathers. Photo from Michael James B. Herrera, UPD School of Archaeology.
The chickens of the Sulu Archipelago were classified into 5 of the 13 known chicken haplogroups, specifically haplogroups A, B, C, D, and E. Haplogroup D was the most prevalent in the region, at 56.79%, and is thought to represent the initial chicken lineage, as well as the most frequent and diverse lineage in ISEA. This was followed by haplogroup B, at 28.81%; while the others occurred much more infrequently.
After comparisons with datasets from neighboring regions and the rest of the Philippines, the team found that the Haplogroup D chickens of Sulu showed a much closer genetic relationship with chickens from Borneo, Sulawesi, and Sumatra in Indonesia, when compared to chickens from the rest of the Philippines. Knowing this, the team generated what is called a median-joining network among the samples to draw out possible close relationships within a haplogroup.
They found, however, that the genetic structure in these specimens was undifferentiated, meaning that these chicken haplotypes did not cluster into island-specific groups. This suggests the active and “cumulative long-term interactions of the different communities within the region, either through trade or migration, over an extended period.” In other words, rather than clustering neatly by island, chickens from different islands were genetically mixed, hinting at a long history of circulation and exchange by their inhabitants.
(A) Map of Island Southeast Asia from the paper showing the inferred gene flow of chickens, pigs, and dogs across the region. (B) The map also highlights distribution of shared cultural elements, including chicken-based dishes, ritual practices, visual art motifs (e.g., okir), and rock art. Together, these layers illustrate the intertwined movement of animals, people and cultural traditions throughout Island Southeast Asia and into the Pacific. Photo from Michael James B. Herrera, UPD School of Archaeology.
Another insight resulted when analyzing the D Haplotypes from Sulu with datasets, the Philippines and the Pacific. Polynesian chickens were seen to carry a specific motif of 4 distinct mutations in their DNA, which acts like a genetic calling card. This motif exists both in Polynesia and in other areas of the Philippines, especially in Luzon and the Visayas, and especially via Haplotype 61. It does not appear in any of the Haplogroup D chickens in Sulu, meaning these chickens come from a completely distinct maternal line.
Moreover, parallel linguistic evidence indicates that the Proto-Austronesian language (associated with Taiwan) had no word for “chicken;” whereas the word emerges in Proto-Malayo-Polynesian, which developed in the Philippines. This is a clue that the Philippines, especially the northern regions like Luzon, emerges as a likelier genetic and cultural launching point for both chickens and their human voyagers that then spread eastward.
Body feathers were specifically taken by Herrera and his team, and not flight or tail feathers, because these take longer to digest by enzymes during DNA extraction. This was done quickly so as not to disrupt the lives of chicken owners. Photo from Michael James B. Herrera, UPD School of Archaeology.
“This study is important because it enhances our understanding of prehistoric and historic human migration, cultural exchange, and animal domestication in the Sulu Archipelago, a key but under-studied region in ISEA,” said Herrera. “It sheds light on the deep and distinct connections between the southern Philippines and Indonesia, challenges assumptions of cultural uniformity across the Philippines, and demonstrates the power of genetic evidence to unlock past human behaviors. For archaeologists and Filipinos alike, it opens new pathways to explore identity, heritage, and regional interconnectedness.”
Joining Herrera in this study are: Fairuz Bangahan, Mark Laurence Garcia, and Michelle Eusebio from the School of Archaeology; John Meldwin Cuales, Jae Joseph Russell B. Rodriguez, Jazelyn Salvador, and Maria Corazon A. De Ungria from the UP Natural Sciences Research Institute DNA Analysis Laboratory; Raquel O. Rubio of the NSRI’s Biological Research and Services Laboratory; Richard N. Muallil from the Mindanao State University – Tawi-Tawi College of Technology and Oceanography; and Rolly Urriza of the National Museum of Natural History’s Ornithology Section.
Read the original paper published in Royal Society Open Science here.
Cover photo by Mar Lopez, UP-MCO
