Data from: A laser-equipped tunnel for the assessment of multiple burst swimming traits in fishes

<p>Burst swimming performance in fishes is relatively understudied despite its critical role in predation attempts and prey evasion, spawning events, and passing hydraulic challenges. Burst swimming is characterized by fast acceleration, over a short distance and of limited duration. The bulk of fast-start performance research uses analysis of high-speed recordings of fish behavior. While behavioral video analysis has improved, it is still expensive in both processing time and computational resources. Here we introduce a laser-gated burst tunnel that improved upon past designs by introducing an adjustable number of lasers (≤ 25) that facilitated greater resolution on burst performance as well as novel laser arrangements facilitating novel performance metrics (e.g., fatigue rate, burst capacity). We quantified the burst velocity, burst capacity and fatigue rate of rainbow trout (<em>Oncorhynchus mykiss</em>), a widely distributed and studied species. We directly compared the results measured by our device to simultaneously collected high-speed camera data and find the velocity estimates to be highly accurate (R<sup>2</sup><sub> </sub>= 0.97). We also compared the burst performance of individual rainbow trout with their individual U<sub>CRIT,</sub> a commonly measured metric of aerobic swimming performance. We found little correlation between the two traits, indicating that fish capable of rapid burst swimming are not necessarily fast sustained swimmers. Finally, we defined and quantified two novel traits of burst swimming performance: burst capacity (the number of burst events that can be elicited prior to performance decline), and fatigue rate (the rate of decline associated with repeated bursting). The burst tunnel is an adjustable platform for quantifying understudied elements of fish swimming physiology, improving design of fish passage technology, and facilitating discoveries in how burst swimming performance changes with environmental conditions.</p><p>Funding provided by: University of California, Agricultural Experiment Station*<br>Crossref Funder Registry ID: <br>Award Number: 2098-H</p><p>Funding provided by: California Sea Grant<br>Crossref Funder Registry ID: https://ror.org/02yn1nr06<br>Award Number: 19054</p><p>Funding provided by: State Water Resources Control Board<br>Crossref Funder Registry ID: http://dx.doi.org/10.13039/100004814<br>Award Number: 20-036-300</p><p>This dataset was collected using a novel burst swimming performance tunnel. The Python script which controls the Raspberry Pi and collects data from the burst tunnel is included. Also included is the processing R script which converts the output of the Raspberry Pi into velocity measurements for each fish's burst performance. </p&gt

Data from: A laser-equipped tunnel for the assessment of multiple burst swimming traits in fishes

<p>Burst swimming performance in fishes is relatively understudied despite its critical role in predation attempts and prey evasion, spawning events, and passing hydraulic challenges. Burst swimming is characterized by fast acceleration, over a short distance and of limited duration. The bulk of fast-start performance research uses analysis of high-speed recordings of fish behavior. While behavioral video analysis has improved, it is still expensive in both processing time and computational resources. Here we introduce a laser-gated burst tunnel that improved upon past designs by introducing an adjustable number of lasers (≤ 25) that facilitated greater resolution on burst performance as well as novel laser arrangements facilitating novel performance metrics (e.g., fatigue rate, burst capacity). We quantified the burst velocity, burst capacity and fatigue rate of rainbow trout (<em>Oncorhynchus mykiss</em>), a widely distributed and studied species. We directly compared the results measured by our device to simultaneously collected high-speed camera data and find the velocity estimates to be highly accurate (R<sup>2</sup><sub> </sub>= 0.97). We also compared the burst performance of individual rainbow trout with their individual U<sub>CRIT,</sub> a commonly measured metric of aerobic swimming performance. We found little correlation between the two traits, indicating that fish capable of rapid burst swimming are not necessarily fast sustained swimmers. Finally, we defined and quantified two novel traits of burst swimming performance: burst capacity (the number of burst events that can be elicited prior to performance decline), and fatigue rate (the rate of decline associated with repeated bursting). The burst tunnel is an adjustable platform for quantifying understudied elements of fish swimming physiology, improving design of fish passage technology, and facilitating discoveries in how burst swimming performance changes with environmental conditions.</p><p>Funding provided by: University of California, Agricultural Experiment Station*<br>Crossref Funder Registry ID: <br>Award Number: 2098-H</p><p>Funding provided by: California Sea Grant<br>Crossref Funder Registry ID: https://ror.org/02yn1nr06<br>Award Number: 19054</p><p>Funding provided by: State Water Resources Control Board<br>Crossref Funder Registry ID: http://dx.doi.org/10.13039/100004814<br>Award Number: 20-036-300</p><p>This dataset was collected using a novel burst swimming performance tunnel. The Python script which controls the Raspberry Pi and collects data from the burst tunnel is included. Also included is the processing R script which converts the output of the Raspberry Pi into velocity measurements for each fish's burst performance. </p&gt

Variation in Thermal Physiology Among Chinook Salmon Populations

Understanding the variations that exist between organisms, populations, and species can provide valuable insight into the evolutionary and environmental drivers relevant to organism fitness. Developing this understanding is critical in an era of rapid environmental change, where effective conservation and management efforts must predict the response of organisms to future, novel environmental conditions.Pacific salmonids are widely considered at-risk from anthropogenic and climatic changes. Additionally, Pacific salmonids exhibit a semelparous anadromous life-history strategy which limits gene-flow and promotes the formation of distinct populations. My first chapter reviews the literature on the thermal physiology of Chinook salmon (Oncorhynchus tshawytscha) from the Central Valley of California, which are the southernmost native populations in the world. I found very little prior research studying interpopulation in thermal physiology among Chinook salmon, despite a vast literature demonstrating the capacity for interaction between thermal physiology and a salmonid’s local environment. I propose a place-based management paradigm which combines both and organisms fundamental and ecological thermal physiology. My second and third chapters employed a common-garden experimental design and several physiological metrics to assess the thermal physiology and acclimation capacity of eight hatchery populations of Chinook salmon from the west coast of North America. All eight populations were reared at the same suite of acclimation temperatures (11, 16 and 20°C) and assessed using five physiological metrics, (growth rate, critical thermal maximum, routine and maximum metabolic rate and aerobic scope). The second chapter aimed to determine whether the thermal physiology and acclimation capacity of three seasonal runs of Chinook salmon in the Sacramento River watershed (CA) differed. I identified quantifiable population differences in CTM, growth, and metabolism among the studied populations and found compelling evidence that the critically endangered Sacramento River winter-run exhibits growth and metabolic capacities indicative of mal-adaptive physiological plasticity to warm temperatures. The final chapter studied six populations of fall-run Chinook salmon and assessed statistical associations between the five physiological traits and 15 environmental predictors to test hypotheses of local adaptation and countergradient variation. My results support local adaptation, wherein populations from warmer habitats exhibit higher critical thermal maxima and faster growth when acclimated to warm temperatures. Among metabolic traits I also found positive associations between migration distance and metabolic capability, indicating that populations with longer migrations may have higher metabolic capacity. Collectively, my research demonstrates that populations of Chinook salmon differ in their thermal physiology and that these differences can be associated with aspects of their environment consistent with hypotheses of local adaptation. With this understanding, one-size-fits-all management frameworks are poised to underserve unique or unusual populations. Instead, place-based population-specific strategies would best serve at-risk populations like the Sacramento River winter-run Chinook salmon

clean_nodC_field2015_OTU_seqs

OTU sequences of nodC genotypes measured on nodules from experimental plants in the field

field_cooccurrence_data

Field Co-occurrence Data for 3 Trifolium specie

soil_chemistry

Soil chemistry data in relation to the distribution of our three Trifolium species

fuc_mdn_nodC_field2015

OTU counts of nodC genotypes measured on nodules from experimental plants in the field