An eDNA window into larval fish habitat, ecosystem structure, and function using CalCOFI data


About the Project

Most marine fishes and invertebrates produce high abundances of tiny larvae that, depending on the species, reside in the open ocean for weeks to months. Mortality is incredibly high (often upwards of 99%) for most fishes during the larval stage but because larvae are so abundant small changes in rates of survival result in orders of magnitude difference in survival to adult stages (i.e., recruitment). For this reason, elucidating the actual mechanisms in the ocean that affect larval survival is an integral component of fisheries management. Yet, despite over a century of recruitment research, accurately estimating these parameters has been difficult and predicting conditions that facilitate larval survival and drive recruitment remains the fundamental challenge in fisheries science and management.

CalCOFI data include physical, environmental, and biological measurements collected from water samples and tows from ship cruises conducted quarterly since ~1950. Measurements are: (i) georeferenced – taken at recorded spatial coordinates; (ii) longitudinal – taken repeatedly over time; (iii) profiled – recorded across depth in the water column; and (iv) multivariate. The complexity of the datasets due to these attributes presents both promise for discovery and challenges for data analysis and display.

This project will aim to ascertain predictive relationships between environmental and biological systems. Focus on the relationship between environmental DNA and fish larvae is anticipated, but students will have some latitude to shape the direction of their work and may utilize secondary datasets as appropriate to the overall project aim. The primary objectives for this project will be: (i) developing interactive data displays effective for exploratory analysis and communication; and (ii) applying statistical methodology for prediction of variables of interest. Students will work primarily in R with version control.


  Student Team

  • Yuqing "Summer" Xia
  • Kassandra Trejo-Zamora


  • Erin Satterthwaite, CalCOFI
  • Trevor Ruiz, UCSB


About CalCOFI

The California Cooperative Oceanic Fisheries Investigations (CalCOFI) are a unique partnership of the California Department of Fish & Wildlife, NOAA Fisheries Service and Scripps Institution of Oceanography. The organization was formed in 1949 to study the ecological aspects of the sardine population collapse off California. Today our focus has shifted to the study of the marine environment off the coast of California, the management of its living resources, and monitoring the indicators of El Nino and climate change. CalCOFI conducts quarterly cruises off southern & central California, collecting a suite of hydrographic and biological data on station and underway. Data collected at depths down to 500 meters include: temperature, salinity, oxygen, phosphate, silicate, nitrate and nitrite, chlorophyll, transmissometer, PAR, C14 primary productivity, phytoplankton biodiversity, zooplankton biomass, and zooplankton biodiversity.

In 2004, the CalCOFI surveys became part of the LTER (Long Term Ecological Research) ecological studies network as a site to understand the pelagic ecosystem of the California Current....