Diffuse phenotypic structure in native chickens across Java and Wallacea is consistent with human-mediated connectivity and decentralised selection
- 1Faculty of Animal Science, Universitas Sebelas Maret, Surakarta 57126, Indonesia
Abstract
Objective: This study aimed to investigate morphometric and plumage-colour variation among native chickens from Wallacea and Java, Indonesia, and to evaluate the contributions 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 decentralised 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.
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BibTeX
@misc{widyas2026diffuse,
title = {{Diffuse phenotypic structure in native chickens across Java and Wallacea is consistent with human-mediated connectivity and decentralised selection}},
author = {N. Widyas and S. Fiddaman and S. Prastowo and A. Ratriyanto and L. A. F. Frantz and R. Drinkwater and R. Kusumaningrum and A. E. T. Sulfiar and E. Wera and P. M. Bulu and Sulasmi and P. R. Matitaputty and T. S. S. Panjaitan and R. Widyastuti and A. Setiaji and A. B. Dharmayanthi and A. Pratiwi and L. A. Pradista and T. Nugroho and Z. A. Wahid and G. Pambuko and E. D. Novitasari and A. D. Sayogo and A. L. Smith},
howpublished = {bioRxiv},
year = {2026},
month = sep,
doi = {10.64898/2026.09.08.750014},
url = {https://www.biorxiv.org/content/10.64898/2026.09.08.750014v1},
note = {CC BY},
}
RIS
TY - UNPB
TI - Diffuse phenotypic structure in native chickens across Java and Wallacea is consistent with human-mediated connectivity and decentralised selection
AU - N. Widyas
AU - S. Fiddaman
AU - S. Prastowo
AU - A. Ratriyanto
AU - L. A. F. Frantz
AU - R. Drinkwater
AU - R. Kusumaningrum
AU - A. E. T. Sulfiar
AU - E. Wera
AU - P. M. Bulu
AU - Sulasmi
AU - P. R. Matitaputty
AU - T. S. S. Panjaitan
AU - R. Widyastuti
AU - A. Setiaji
AU - A. B. Dharmayanthi
AU - A. Pratiwi
AU - L. A. Pradista
AU - T. Nugroho
AU - Z. A. Wahid
AU - G. Pambuko
AU - E. D. Novitasari
AU - A. D. Sayogo
AU - A. L. Smith
PY - 2026
DA - 2026/09/08
PB - bioRxiv
DO - 10.64898/2026.09.08.750014
UR - https://www.biorxiv.org/content/10.64898/2026.09.08.750014v1
AB - Objective: This study aimed to investigate morphometric and plumage-colour variation among native chickens from Wallacea and Java, Indonesia, and to evaluate the contributions 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 decentralised 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.
ER -