Diffuse phenotypic structure in native chickens across Java and Wallacea is consistent with human-mediated connectivity and decentralised selection

A recent study has examined the phenotypic variation among native chickens from Wallacea and Java, Indonesia. The researchers collected samples from 259 households spread across eight provinces. They gathered data on production systems and farmer selection practices through structured surveys. Using principal component analysis, permutational multivariate analysis of variance, and hierarchical variance partitioning, the team examined the variation in morphometric traits and plumage coloration across locations, provinces, and islands.

The researchers found significant differences in several morphometric traits among the sampled populations, with differences detected across provinces and islands. However, they also observed extensive overlap in both morphometric and plumage-colour space, indicating a diffuse structuring rather than discrete groups. Within each location, variation accounted for the largest proportion of total phenotypic variance for most traits.

This suggests decentralized smallholder management practices and continued human-mediated exchange among populations.

The study concludes that geographic fragmentation and agroecological heterogeneity alone are not enough to create strongly differentiated phenotypic groups when connectivity among populations is maintained. The researchers suggest that further investigation using genomic data is necessary to determine if the observed phenotypic connectivity corresponds to contemporary gene flow, the retention of ancestral variation, or convergent environmental responses.