Sequencing of captive red junglefowls in zoological parks in Japan

How population demography shapes the genomic landscape is a central question in domestication genomics and conservation genetics. Although bottlenecked populations are characterized by reduced genetic diversity and accumulation of deleterious mutations, how these genomic landscapes were shaped in the early stages of domestication remains poorly understood. Captive red junglefowl populations in zoological parks represent a unique model for exploring these early domestication processes. These populations originate from recent introductions from the wild, are maintained at small sizes, and are isolated from active breeding programs, making them ideal for studying the interplay between demographic history and genome evolution under captivity. In this study, we newly sequenced the captive population of red junglefowls from multiple zoological parks to perform comparative population genomic analysis with wild red junglefowls and domesticated chicken breeds.

种群人口统计学如何塑造基因组景观（genomic landscape），是驯化基因组学（domestication genomics）与保护遗传学（conservation genetics）领域的核心科学问题之一。尽管经历瓶颈效应的种群（bottlenecked populations）普遍表现为遗传多样性降低与有害突变（deleterious mutations）累积，但驯化早期阶段这些基因组景观的具体形成机制仍有待阐明。动物园内圈养的红原鸡（red junglefowl）种群，为探索此类早期驯化过程提供了独特的研究模型。此类种群均由近期野外个体引种而来，种群规模长期维持于较小水平，且与现有育种项目相互隔绝，使其成为研究圈养条件下种群历史（demographic history）与基因组演化（genome evolution）之间互作关系的理想体系。本研究对多个动物园的圈养红原鸡种群开展了全新测序，并将其与野生红原鸡及驯化家鸡品种进行群体基因组比较分析。