Diffuse phenotypic structure in native chickens across Java and Wallacea is consistent with human-mediated connectivity and decentralized selection
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Objective
This study aimed to investigate morphometric and plumage-colour variation among native chickens from Wallacea and Java, Indonesia, and to evaluate the contribution of geographic and production-system factors to phenotypic diversity.
Methods
Native chickens were sampled from 259 households across eight provinces in Indonesia. Household-level information on production systems and farmer selection practices was collected through structured surveys. Morphometric traits and HSV-derived plumage-colour variables were analysed using principal component analysis (PCA), permutational multivariate analysis of variance (PERMANOVA), and hierarchical variance partitioning to assess phenotypic variation across locations, provinces, and islands.
Results
Substantial phenotypic variation was observed among sampled populations, with significant province-and island-level differences detected for several morphometric traits. However, extensive overlap among locations was evident in both morphometric and plumage-colour space, indicating diffuse rather than discrete structuring. Within-location variation accounted for the largest proportion of total phenotypic variance across most traits, consistent with decentralized smallholder management and continued human-mediated exchange.
Conclusion
Geographic fragmentation and agroecological heterogeneity alone appear insufficient to generate strongly differentiated phenotypic groups when connectivity among populations is maintained. Whether this phenotypic connectivity corresponds to contemporary gene flow, retained ancestral variation, or convergent environmental responses remains to be tested using genomic data.
Implications
This study shows that native chickens in Indonesia maintain high diversity despite being raised across different islands and environments. The findings support protecting local chicken resources that underpin smallholder livelihoods, rural food security, and cultural traditions, and can help future breeding and conservation programs develop chickens better adapted to local climates, diseases, and farming conditions: improving farmer income and sustainable local poultry production.
