Our research group focuses on applied questions in fisheries management and conservation biology. Our approaches to these questions are varied, but typically involve both fieldwork and analytic techniques. We maintain active field programs both locally, and in the tropics. Lab members have particular strengths in quantitative theory and tools, including stock assessment, time series analysis, mark-recapture analysis, and stable isotope mixing model theory and methods.


Grouper Moon Project: Studying a Caribbean Icon

grouper moon image

The Grouper Moon Project is a collaborative conservation program between Reef Environmental Education Foundation (REEF), the Cayman Islands Department of the Environment, and Scripps Institution of Oceanography studying Nassau Grouper (Epinephelus striatus) – a social and ecological corner stone of Caribbean’s coral reefs. The research focuses on Little Cayman, which has one of the largest (and one of just a few) known spawning aggregations of Nassau Grouper in the Caribbean. Over 4,000 individuals “group” at a single location for ~10 days following winter full moons. Since the project’s inception in 2002, Brice Semmens has been a lead scientist on the project.

The research team has coordinated annual efforts to monitor and study the aggregation. The project has grown in scope to include: Nassau Grouper Education Program, Baby Grouper Adrift! Satellite Drifter Project, Marine Protected Areas and Spawning Aggregation research, and an ambient acoustics research program.

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Population Structure and Conservation of Oceanic Manta Rays

Oceanic Manta Rays (Manta birostris) are increasingly caught in targeted fisheries for their gill rakers, fueled by demand as a pseudo-remedy in traditional Chinese medicine. Given extremely low reproductive rates, even small artisanal fisheries and bycatch will have significant impacts on manta populations, while large-scale targeted fisheries may lead to population decline and perhaps local extinctions. Understanding the basic ecology and population dynamics of the species is a prerequisite to developing effective conservation and management strategies for the species. Semmens Lab Ph.D. student Josh Stewart is investigating the population structure and spatial ecology of oceanic manta rays in the Indo-Pacific using a diversity of techniques to identify space use, migratory corridors, regional subpopulations and connectivity between oceanic manta hotspots and aggregations.

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The Coast Angler Tagging Cooperative

The Coastal Angler Tagging Cooperative is a partnership between the recreational fishing community, California Department of Fish and Wildlife, San Diego Oceans Foundation, and Scripps Institution of Oceanography. We are working together to measure population dynamics of three highly important marine bass species in the genus Paralabrax. We are integrating tag-recapture and acoustic telemetry methods to quantify population abundance, growth, mortality, and movement patterns of the three species in southern California.

With help from thousands of recreational anglers, we will use this essential information in future stock assessments.

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Stable Isotope Analysis

Brice Semmens and his colleagues develop and refine Bayesian methods for stable isotope mixing model analyses. They first described a novel Bayesian framework (MixSIR) for mixing model analysis that incorporated uncertainty in the isotopic signatures of both predators (mixtures) and prey (sources) in two Ecology Letters publications in 2008 and 2009. In 2011, Semmens et al. published a hierarchical version of the mixing model formulation that incorporates individual (and group-level) diet variability among predators, and demonstrates how to use information theoretic approaches to evaluate data support for alternate mixing model parameterizations. Semmens Lab Ph.D. student, Brian Stock is currently developing MixSIAR, a GUI tool that incorporates recent developments in mixing model tools. MixSIAR represents a collaborative effort between many of the researchers involved in developing mixing model theory to date.

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Ecological and Evolutionary Effects on Fish Recruitment

Variation in population replenishment via larval settlement (recruitment) is a hallmark of many marine fish populations and a major driver of variation in the subsequent abundance of juveniles and adults. For decades fisheries biologists have referred to ‘the recruitment problem’ as the major challenge to our understanding of fish population dynamics and a persistent obstacle to effective management. Semmens Lab Post-Doc Researcher, Darren Johnson is studying how recruitment variability can be better understood by incorporating evolutionary processes (especially selective mortality) into traditional, density-dependent models of recruitment. A central premise of Darren’s research is that although density-dependent processes are important, phenotypic variation (in concert with environmental heterogeneity) can lead to major changes in survival and recruitment.

Recent publication:

Phenotypic variation and selective mortality as major drivers of recruitment variability in fishes. DW Johnson, K Grorud‐Colvert, S Sponaugle, BX Semmens. Ecology letters, 17 (6), 743-755