Data from: Effectiveness of managed gene flow in reducing genetic divergence associated with captive breeding

Captive breeding has the potential to rebuild depressed populations. However, associated genetic changes may decrease restoration success and negatively affect the adaptive potential of the entire population. Thus, approaches that minimize genetic risks should be tested in a comparative framework over multiple generations. Genetic diversity in two captive-reared lines of a species of conservation interest, Chinook salmon (Oncorhynchus tshawytscha), was surveyed across three generations using genome-wide approaches. Genetic divergence from the source population was minimal in an integrated line, which implemented managed gene flow by using only naturally-born adults as captive broodstock, but significant in a segregated line, which bred only captive-origin individuals. Estimates of effective number of breeders revealed that the rapid divergence observed in the latter was largely attributable to genetic drift. Three independent tests for signatures of adaptive divergence also identified temporal change within the segregated line, possibly indicating domestication selection. The results empirically demonstrate that using managed gene flow for propagating a captive-reared population reduces genetic divergence over the short term compared to one that relies solely on captive-origin parents. These findings complement existing studies of captive breeding, which typically focus on a single management strategy and examine the fitness of one or two generations.

人工繁育（captive breeding）有望恢复种群数量衰退的物种群体。然而，伴随产生的遗传改变可能降低复育成功率，并对整个种群的适应潜力产生负面影响。因此，应在多世代的比较框架下测试能够最小化遗传风险的繁育策略。本研究针对一种具有保护价值的物种——奇努克鲑鱼（Chinook salmon, *Oncorhynchus tshawytscha*）的两个人工繁育品系，采用全基因组分析方法（genome-wide approaches）对其连续三个世代的遗传多样性进行了检测。相较于仅以圈养出生个体作为繁育亲鱼的隔离品系，实施了管理式基因流（managed gene flow）策略（仅将野外自然出生的成体作为圈养繁育亲鱼）的整合品系，其与源种群的遗传分化程度极低；而隔离品系则表现出显著的遗传分化。有效繁殖种群数（effective number of breeders）的估算结果显示，隔离品系所观察到的快速遗传分化，在很大程度上可归因于遗传漂变（genetic drift）。三项独立的适应性分化（adaptive divergence）特征检测分析也发现，隔离品系内部存在随时间推移的遗传变化，这可能暗示存在驯化选择（domestication selection）作用。本研究结果从实验层面证实：相较于仅依赖圈养出生亲鱼的繁育策略，采用管理式基因流进行人工种群扩繁，可在短期内降低与源种群的遗传分化水平。现有多数人工繁育相关研究通常仅聚焦单一管理策略，且仅考察1至2个世代的适合度，本研究结果可作为对该类研究的重要补充。