Size-selective mortality induces evolutionary changes in group risk-taking behavior and the circadian system in a fish

1. Intensive and trait-selective mortality of fish and wildlife can cause evolutionary changes in a range of life-history and behavioral traits. These changes might in turn alter the circadian system due to coevolutionary mechanisms or correlated selection responses both at behavioral and molecular levels, with knock-on effects on daily physiological processes and behavioral outputs.

2. We examined the evolutionary impact of size-selective harvesting on group risk-taking behavior and the circadian system in a model fish species. We exposed zebrafish (Danio rerio) to either large or small size-selective harvesting relative to a control over five generations, followed by eight generations during which harvesting halted to remove maternal effects.

3. Size-selective mortality affected fine-scale timing of behaviors. In particular, small size-selective mortality, typical of specialized fisheries and gape-limited predators targeting smaller size classes, increased group risk-taking behavior during feeding and after simulated predator attacks. Moreover, small size-selective mortality increased early peaks of daily activity as well as extended self-feeding daily activity to the photophase compared to controls. By contrast large size-selective mortality, typical of most wild capture fisheries, only showed an almost significant effect of decreasing group risk-taking behavior during the habituation phase and no clear changes in fine-scale timing of daily behavioral rhythms compared to controls.

4. We also found changes in the molecular circadian core clockwork in response to both size selective mortality treatments. These changes disappeared in the clock output pathway because both size-selected lines showed similar transcription profiles. This switch downstream to the molecular circadian core clockwork also resulted in similar overall behavioral rhythms (diurnal swimming and self-feeding in the last hours of darkness) independent of the underlying molecular clock.

5. To conclude, our experimental harvest left an asymmetrical evolutionary legacy in group risk-taking behavior and in fine-scale daily behavioral rhythms. Yet, the overall timing of activity showed evolutionary resistance probably maintained by a molecular switch. Our experimental findings suggest that size-selective mortality can have consequences for behavior and physiological processes.

Methods
This dataset contains several data related to Zebrafish (Danio rerio):

- behavioral data regarding risk-taking behavior (i.e., time spent at the surface of the water as recorded by automated video image tracking).

- behavioral data regarding activity rhythms recorded using infrared sensors

- gene expression

- Standard lenght of fish

The dataset is organized in an excel file with the following sheets:

1) diving_test

- Line: the selection line

- Rep: the replicate of each selection line

- Group: the group which is the experimental unit

- Trial: the different trials

- Time: Time within each trial (30-s bins)

- Surf_time: Cumulative time spent at the surface

2) activity_rhythms

- PHENOTYPE: swimming or self feeding

- PHASE: first or second light-dark phase

- TIME: time within each 24-h light-dark phase (10 min bin)

- LIGHT: 0 = dark; 1 = light

- LINE: the selection line

- ACT: total activity

- se.up: standard error up

- se.down: standard error down

3) mesor_noct

- PHENOTYPE: swimming or self feeding

- LINE: the selection line

- LINE.REP: the replicate of each selection line

- GROUP: the group which is the experimental unit

- PHASE: first or second light-dark phase

- MESOR: the midline estimating statistic of rhythm

- Area: area under the waveform curve, AUC

- E_At: early daily activity (percentage of activity during the first four hours of light)

4) feeding

- LINE: the selection line

- LINE.REP: the replicate of each selection line

- GROUP: the group which is the experimental unit

- PHASE: first or second light-dark phase

- TIME: from to two hours before light-on (1) to one hour after light-on (4), including cumulative level (ALL)

- A: area under the waveform curve, AUC

5) input_R_circadian

- LINE: the selection line

- REP: the replicate of each selection line

- TISSUE: B = brain; L = liver

- TIME: sampling time (24 h)

- From column E to column Q: RTqPCR readings

6) standard_length

- DPF: days post fertilization

- LINE: the selection line

- REP: the replicate of each selection line

- GROUP: the group which is the experimental unit

SL.cm: individual standard length within the group

1. 鱼类与野生动物的高强度、性状选择性死亡，可引发一系列生活史与行为性状的演化改变。这类变化可能通过协同演化机制，或行为与分子层面的相关性选择响应，进而改变昼夜节律系统，并对每日生理过程与行为输出产生连锁效应。

2. 本研究以模式鱼类为对象，探究了体型选择性捕捞对群体冒险行为与昼夜节律系统的演化影响。我们将斑马鱼（Danio rerio）分为三组：对照组、大体型选择性捕捞组与小体型选择性捕捞组，历经5代选择养殖，随后暂停捕捞8代以消除母本效应。

3. 体型选择性死亡会影响行为的精细时间节律。具体而言，以小型个体为目标的特化渔业与口限捕食者所对应的小体型选择性死亡，会提升斑马鱼在摄食阶段与模拟捕食攻击后的群体冒险行为。与对照组相比，小体型选择性死亡还会提升每日活动的早期峰值，并将自主摄食活动时段延长至光照期。相较之下，代表多数野生捕捞渔业的大体型选择性死亡，仅在习惯化阶段表现出近乎显著的群体冒险行为降低效应，且与对照组相比，每日行为节律的精细时间节律无明显变化。

4. 我们还发现，两种体型选择性死亡处理均会引发分子核心生物钟的改变。但两类选择系的转录谱一致，使得这类变化在生物钟输出通路中消失。这种分子核心生物钟下游的调控转换，还使得整体行为节律（黑暗最后时段的昼行性游泳与自主摄食行为）保持一致，且不受底层分子生物钟的影响。

5. 综上，本实验性捕捞对群体冒险行为与每日行为的精细时间节律造成了非对称的演化遗留效应。但活动的整体时间节律表现出演化抗性，这一抗性可能由分子开关维持。本实验结果表明，体型选择性死亡可对行为与生理过程产生影响。

### 数据集说明
本数据集包含与斑马鱼（Danio rerio）相关的多类数据：
- 冒险行为相关行为数据：即通过自动化视频图像追踪记录的鱼类在水面停留时长。
- 活动节律相关行为数据：通过红外传感器记录所得。
- 基因表达数据。
- 鱼类标准体长数据。

本数据集以Excel文件组织，包含以下工作表：

1) 潜水测试（diving_test）
- Line：选择系
- Rep：各选择系的重复样本
- Group：作为实验单元的组别
- Trial：不同实验试次
- Time：每个试次内的时间（以30秒为时间窗）
- Surf_time：鱼类在水面的累计停留时长

2) 活动节律（activity_rhythms）
- PHENOTYPE：表型，包括游泳活动与自主摄食活动
- PHASE：光暗周期阶段，包括第一光暗周期与第二光暗周期
- TIME：24小时光暗周期内的时间（以10分钟为时间窗）
- LIGHT：光照状态，0代表黑暗，1代表光照
- LINE：选择系
- ACT：总活动量
- se.up：标准误上限
- se.down：标准误下限

3) 中值节律（mesor_noct）
- PHENOTYPE：表型，包括游泳活动与自主摄食活动
- LINE：选择系
- LINE.REP：各选择系的重复样本
- GROUP：作为实验单元的组别
- PHASE：光暗周期阶段，包括第一光暗周期与第二光暗周期
- MESOR：节律中值（midline estimating statistic of rhythm）
- Area：波形曲线下面积（AUC，即Area Under Curve）
- E_At：早期每日活动量（光照前4小时的活动占比）

4) 摄食活动（feeding）
- LINE：选择系
- LINE.REP：各选择系的重复样本
- GROUP：作为实验单元的组别
- PHASE：光暗周期阶段，包括第一光暗周期与第二光暗周期
- TIME：时间范围为开灯前2小时至开灯后1小时，共分为4个时段，同时包含累计水平（ALL）
- A：波形曲线下面积（AUC，即Area Under Curve）

5) 昼夜节律输入数据（input_R_circadian）
- LINE：选择系
- REP：各选择系的重复样本
- TISSUE：组织类型，B代表脑组织，L代表肝组织
- TIME：采样时间（24小时制）
- E列至Q列：实时定量PCR（RTqPCR）检测读数

6) 标准体长（standard_length）
- DPF：受精后天数（days post fertilization）
- LINE：选择系
- REP：各选择系的重复样本
- GROUP：作为实验单元的组别
- SL.cm：组内个体的标准体长（单位：厘米）