Abstract: Heat-stress resilience is vital for poultry in tropical/subtropical regions where
high temperatures impair productivity. Ake chickens, as the only naked-neck chicken breed
in China, exhibit robust resistance to heat stress, but this breed lacks clarity in its genetic
origins. This study utilized the next-generation sequencing data from 22 chicken breeds
to conduct phylogenetic and population analyses. Gene flow analysis revealed a gene
migration event from Iranian naked-neck chickens and Indian local breeds to Ake chickens,
and population separation estimates suggested that the naked-neck gene was introduced to
China around 500–600 years ago. NJ-tree, PCA, and population structure analyses showed
that Ake chickens cluster with Yunnan native breeds, which diverged only 100–200 years
ago. A selective sweep in the candidate region on chromosome 3 (97.0–97.37 Mb) showed
elevated genetic differentiation (FST) and educed nucleotide diversity (π) compared to
the genome-wide average, indicating rapid fixation of the trait under natural/artificial
selection. Demographic reconstruction indicated that the current effective size of Ake
chickens is stable at 2000–3000 individuals. These findings deepen our understanding of
Ake chicken evolution and provide valuable insights for conservation and the development
of heat-stress-resistant poultry breeds.