Abstract：
Intraspecific biodiversity is vital for species persistence in an increasingly volatile world. By embracing methods that integrate information at different spatiotemporal scales, we can directly monitor and reconstruct changes in intraspecific biodiversity. Here we combined genetics and otolith biochronologies to describe the genotypic and phenotypic diversity of Chinook salmon (Oncorhynchus tshawytscha) in the Yuba River, California, comparing cohorts that experienced a range of hydroclimatic conditions. Yuba River salmon have been heavily impacted by habitat loss and degradation, and large influxes of unmarked hatchery fish each year have led to concern about introgression and uncertainty around the viability of its wild populations, particularly the rarer spring-run salmon. Otolith strontium isotopes showed that Yuba River origin fish represented, on average, 42% (range 7%-73%) of spawners across six return years (2009-2011, 2018-2020), with large interannual variability. The remainder of adult Chinook salmon in the river were primarily strays from the nearby Feather River hatchery, and since 2018 from the Mokelumne River hatchery. Among the Yuba-origin spawners, on average, 30% (range 14%-50%) exhibited the spring-run genotype. The Yuba-origin fish also displayed a variety of outmigration phenotypes that differed in the timing and size at which they left the Yuba river. Early-migrating fry dominated the returns (mean 59%, range 33%-89%), and their contribution rates were negatively correlated with freshwater flows. It is unlikely that fry survival rates are elevated during droughts, suggesting that this trend reflects disproportionately low survival of larger later migrating parr, smolts, and yearlings along the migratory corridor in drier years. Otolith daily increments indicated generally faster growth rates in non-natal habitats, emphasizing the importance of continuing upstream restoration efforts to improve in-river growing conditions. Together, these findings show that, despite a long history of habitat degradation and hatchery introgression, the Yuba River maintains intraspecific biodiversity that should be taken into account in future management, restoration, and reintroduction plans. The finding that genotypic spring-run are reproducing, surviving, and returning to the Yuba River every year suggests that re-establishment of an independent population is possible, although hatchery-wild interactions would need to be carefully considered. Integrating methods is critical to monitor changes in key genetic, physiological, and behavioral traits to assess population viability and resilience.
摘要：
在日益动荡的世界中，种内生物多样性对于物种的持久性至关重要。通过采用整合不同时空尺度信息的方法，我们可以直接监测和重建种内生物多样性的变化。在这里，我们结合遗传学和耳石生物年代学来描述尤巴河中奇努克鲑鱼（Oncorhynchustshawytscha）的基因型和表型多样性，加州,比较经历了一系列水文气候条件的队列。浴巴河鲑鱼受到栖息地丧失和退化的严重影响，每年大量未标记的孵化场鱼类的涌入导致人们对其野生种群生存能力的渗入和不确定性的担忧，特别是稀有的春季鲑鱼。Otolith锶同位素表明，尤巴河起源的鱼类代表，平均而言,在六个回归年（2009-2011年、2018-2020年）中，42%（7%-73%）的产卵者，年际变化很大。河中其余的成年奇努克鲑鱼主要来自附近的羽毛河孵化场，自2018年以来，来自Mokelumne河孵化场。在浴霸起源的产卵者中，平均而言,30％（范围14％-50％）表现出春季运行基因型。浴霸起源的鱼还表现出各种向外迁移的表型，它们离开浴霸河的时间和大小有所不同。早期迁移的鱼苗主导了回报(平均59%，范围33%-89%)，它们的贡献率与淡水流量呈负相关。干旱期间鱼苗存活率不太可能提高，这表明这一趋势反映了更大的后期迁徙群体的存活率低得不成比例，Smolts,在干燥的年代，沿着迁徙走廊的一岁。Otolith每日增量表明非出生栖息地的生长速度通常较快，强调继续上游恢复工作以改善河流生长条件的重要性。一起,这些发现表明，尽管栖息地退化和孵化场渗入的历史很长，于巴河保持着种内生物多样性，在未来的管理中应予以考虑，restoration,和重新引入计划。基因型春季运行正在繁殖的发现，幸存下来,每年重返浴巴河表明重建独立的人口是可能的，尽管孵化场与野生的相互作用需要仔细考虑。整合方法对于监测关键基因的变化至关重要，生理,和行为特征来评估种群生存能力和弹性。
