Early evidence for establishment of a Chinook salmon population in a restored watershed

As fish populations face compounding pressures under climate change, highly modified rivers are receiving increasing research and conservation attention as important sites for restoration. Across the North Pacific Ocean, Chinook salmon (Oncorhynchus tshawytscha) have experienced unprecedented declines and extirpations because of habitat loss and fragmentation and climate variability. Here, we studied a rare example of a novel salmon population developing in Putah Creek, California, a dam-controlled stream flowing through an area of intensive agriculture where salmon were unlikely to occur prior to the rehabilitation of a more natural flow regime. We used otoliths from adult Chinook salmon carcasses recovered from Putah Creek to determine river- or hatchery-of-origin for five spawning year classes. Our results provide evidence of successful salmon reproduction, outmigration survival, and natal homing of individuals back to Putah Creek in recent years. Although hatchery-origin fish that s..., , , # Data from: Early evidence for establishment of a Chinook salmon population in a restored watershed ## Description of the data and file structure Files are in a single .zip file and need to be extracted. There is an R project file included and several subfolders that are referenced in the scripts. The `data folder` contains the raw data used for the analyses, the `scripts folder` contains the R scripts, and the `outputs folder` is empty but will be populated with subsequent runs of the scripts. ### **Scripts** All scripts were written in R using R studio and all packages are cited in the text and script files. Scripts are numbered and need to be run in sequence to generate the output files used in subsequent scripts. **01_putah_creek_oto**: Data preparation, homogenization of variable types and names, and fish length and weight analyses **02_putah_creek_data_reduction**: Otolith strontium isotope data reduction. This script makes use of the outputs from isofishR (PC_2017_2021_04...随着鱼类种群在气候变化背景下面临多重叠加压力，高度改造的河流作为重要的生态修复场所，正受到越来越多的研究与保护关注。在北太平洋海域，奇努克鲑鱼（Chinook salmon，学名*Oncorhynchus tshawytscha*）因栖息地丧失与破碎化、气候波动，正经历前所未有的种群下降与局部灭绝。本研究聚焦加利福尼亚州普塔溪（Putah Creek）中罕见的新兴鲑鱼种群案例：该溪流受大坝调控，流经集约化农业区域，在恢复更自然的水文节律之前，这里几乎不可能有鲑鱼栖息。我们利用从普塔溪采集到的成年奇努克鲑鱼尸体的耳石（otolith），对5个产卵龄组的个体进行了河流或孵化场起源的判定。研究结果证实，近年来已有鲑鱼成功完成繁殖、洄游存活，并实现个体返回普塔溪的归巢行为。尽管孵化场起源的个体[...]（原文未完整呈现），# 数据来源：《恢复流域中奇努克鲑鱼种群建立的早期证据》 ## 数据与文件结构说明 所有文件打包于单个ZIP压缩包中，需解压后方可使用。压缩包内包含R项目文件，以及脚本中引用的多个子文件夹：`data文件夹`存放分析所用的原始数据；`scripts文件夹`存放R脚本；`outputs文件夹`初始为空，运行脚本后将生成后续的输出文件。 ### 脚本说明 所有脚本均使用R Studio基于R语言编写，所有依赖包均在正文与脚本文件中注明来源。脚本按序号编号，需按顺序运行以生成后续脚本所需的输出文件。 **01_putah_creek_oto**：数据预处理、变量类型与名称统一化，以及鱼类体长与体重分析 **02_putah_creek_data_reduction**：耳石锶同位素数据处理。本脚本使用了isofishR工具的输出结果（PC_2017_2021_04...，原文未完整呈现）