Sacramento River winter-run Chinook salmon cohort reconstruction – data and code

Maturation schedules shape a population’s age structure and influence productivity and exposure to fishing. Fish cultivated and raised in artificial environments like hatcheries may mature at different ages compared to their natural-origin counterparts. We evaluated whether endangered Sacramento River winter-run Chinook salmon (Oncorhynchus tshawytscha) produced in a conservation hatchery had different maturation schedules compared to natural-origin fish, and how differences affected their exposure to, and impact from, the ocean salmon fishery. Using coded-wire tags collected from hatchery fish in the ocean and in-river fisheries and on the spawning grounds, and scales collected from natural-origin spawner carcasses, we reconstructed the life history of hatchery and natural-origin cohorts from 2002–2015 brood years. Hatchery fish had similar age-2 maturation rates but higher age-3 maturation rates compared to natural-origin fish, resulting in fewer age-4 individuals and an overall more ..., , , # Readme **Scripts** 1\. CWT Spawning Data Prep\.R – Preparing coded\-wire tag recovery data from spawning grounds and hatchery for hatchery\-origin cohort reconstruction 2\. CWT Harvest Data Prep\.R – Preparing coded\-wire tag recovery data from ocean and in\-river harvest\. Calculating the age\-aggregated encounter rate\. 3\. Hatchery Cohort Reconstruction\.R – Cohort reconstruction code for hatchery cohorts from CWT data\. Calculates hatchery\-origin maturation and impact rates\. 4\. Impact rates shared\.R – Calculating impact rates based on encounter rate and average harvestability and release mortality\. 5\. Hatchery Cohort Reconstruction by sex\.R – Sex\-specific cohort reconstruction code for hatchery cohorts using impact rates from hatchery cohort reconstruction\. 6\. Natural Cohort Reconstruction Prep\.R – Age specific escapement based on scale data\. Kimura Chikuni adjustments 7\. Natural Cohort Reconstruction\.R \- Cohort reconstruction code for natural cohorts\. Calculates...成熟时间表塑造种群的年龄结构，并影响其生产力与捕捞暴露风险。在孵化场等人工环境中培育养殖的鱼类，其成熟年龄可能与野生种群存在差异。本研究针对濒危的萨克拉门托河冬季洄游奇努克鲑（*Oncorhynchus tshawytscha*）展开评估：对比保护型孵化场繁育的该物种个体与野生种群是否存在不同的成熟时间表，以及这些差异如何影响其在海洋鲑鱼渔业中的暴露风险与受影响程度。 本研究通过采集海洋、河道渔业及产卵场中孵化场个体的编码线标（coded-wire tag, CWT）数据，以及野生产卵亲体尸体的鳞片样本，重建了2002至2015年繁育年度的孵化场与野生同龄群的生活史。结果显示，与野生种群相比，孵化场个体的2龄成熟率相近，但3龄成熟率更高，导致4龄个体数量更少，整体呈现更为…… # 自述文件（Readme） ## 脚本文件 1. `CWT Spawning Data Prep.R`：处理产卵场与孵化场的编码线标回收数据，用于孵化场来源同龄群的重建 2. `CWT Harvest Data Prep.R`：处理海洋与河道捕捞的编码线标回收数据，计算年龄聚合的遭遇率 3. `Hatchery Cohort Reconstruction.R`：基于编码线标数据重建孵化场来源同龄群的代码，用于计算孵化场个体的成熟率与影响率 4. `Impact rates shared.R`：基于遭遇率、平均捕捞率与放流死亡率计算影响率 5. `Hatchery Cohort Reconstruction by sex.R`：利用孵化场同龄群重建得到的影响率，实现分性别的孵化场同龄群重建代码 6. `Natural Cohort Reconstruction Prep.R`：基于鳞片数据计算年龄特异性逃逸量，并进行木村-奇库尼（Kimura Chikuni）校正 7. `Natural Cohort Reconstruction.R`：野生同龄群的重建代码，用于计算……