Thesis Defense by Christian Denney- December 1, 2017

Characterization of a new stero-video tool to survey deep water benthic fish assemblages with comparison to a remotely operated vehicle

A Thesis Defense by Christian Denney

Fisheries and Conservation Biology Lab

December 1st, 2017

MLML Seminar Room


Christian Graduated from UC Davis in 2009 with a BS in Biology and an interest in population and community dynamics. As an undergraduate, he spent a quarter studying at Bodega Marine Lab where he worked with Dr. Stephen Morgan and PhD candidate Sarah Gravem studying predator-prey interactions. After graduating, he worked for a year with CA Department of Fish and Wildlife monitoring lakes and streams for invasive fish species before joining Rick Starr's Lab at Moss Landing Marine Labs in 2010. At Moss Landing, he studied competitive interactions of juvenile Blue Rockfish (Sebastes mystinus) and worked on the California Collaborative Fisheries Research Program. These experiences in population and community dynamics and fisheries research led him to focus his thesis work on designing the methodology for using a new visual survey tool for monitoring deep water fish assemblages. This research will hopefully lead to improved monitoring for populations that are currently under-studied.

Thesis Abstract:

Increasing use of ecosystem-based management strategies, which are often applied to broad geographic areas and preclude extractive activities, are creating a need for rapid, cost-effective monitoring of large areas. Visual surveys are increasingly being used to meet this need. In this thesis, I examine a new tool for surveying fish assemblages in deep-water habitat: a stereo-video lander. In Chapter 1, I evaluate methodological choices and their impact on the data collected. In Chapter 2, I compare the video lander with a Remotely Operated Vehicle (ROV). In characterizing the new stereo-video lander, I found a negligible effect of bait on the number of fish observed or on the number of species observed. The rotating camera system yielded density estimates slightly lower than those determined by a stationary camera but the rotating camera system produced less variance with the same number of surveys. In comparing the lander and the ROV, both measured similar densities for most species. Furthermore, I found that estimates of the variance in fish density were similar for the two tools given a comparable sampling effort (i.e., number of sites surveyed). Differences in community assemblage were found to be significant between the two tools. Because of the similarity in results and ability to quickly perform surveys and move on to new areas, the lander represents a new option when considering visual tools for deep-water research.

MLML’s Dr. Alison Stimpert co-authored recently published study on blue whale behavior

Dr. Alison Stimpert

Research Faculty member Dr. Alison Stimpert serves a co-author for a large collaborative study on blue whales that has revealed preferences in the direction (right vs left handedness) that the whales will roll during lunge feeding.  The study was published in Current Biology on November 20th, 2017 and featured in UCSC News, as well as The Guardian.  You can download the paper for free for 50 days here.

Advances in the study of foraging behavior of cetaceans from 3D movement and video tags

David Cade, Hopkins Marine Station
Moss Landing Marine Labs Seminar Series - December 7th, 2017

Hosted by the Phycology Lab

MLML Seminar Room, 4pm

Open to the public

David Cade was an educator (6 years in the outdoors and 6 years in a math classroom) before returning to science to pursue his passions. After earning a master’s degree in education at Stanford University in 2005 and a master’s in oceanography at Oregon State University in 2014, Cade is now in the midst of his Ph.D. work in Jeremy Goldbogen’s lab at Stanford University’s Hopkins Marine Station where he studies the foraging ecology of baleen whales. 

Advances in the study of foraging behavior of cetaceans from 3D movement and video tags

For nearly all of human existence on the sea, our understanding of whales has been limited to what we can observe at the surface. For fully aquatic animals such as these, however, time spent on the surface is really a tiny fraction of the life cycle of these largest predators on the planet. Basic questions about feeding behavior and ecology have only begun to be answered in the last fifteen years with the advent of animal-borne sensors capable of logging cetacean behavior underwater. Only in the last three years have sensors that measure orientation and motion been combined with high-quality video cameras to provide us with a whale's eye view of the feeding events that are so critical to overall population recovery from 20th century lows. These devices have allowed old hypotheses to be tested, and new questions and insights have been generated with every new deployment.

Dr. Cailliet (MLML Faculty Emeritus) quoted in a National Geographic article on the challenges of aging sharks

How long do sharks live?  Recent studies using carbon radioisotopes suggest we've been underestimating the ages of sharks, especially older ones.  An article by National Geographic quotes our ichthyologist emeritus, Dr. Gregor Cailliet on the challenges of aging sharks using calcified growth bands:

Gregor Cailliet, professor emeritus at California's Moss Landing Marine Laboratories who has been aging sharks since the 1970s, says the banding method leads to the good, bad, and the ugly.

“The good are the ones where the growth zones and validated ages are identical. The bad is when they don’t mean anything. The ugly are the ones in which there are discrepancies.”

Read the full article here.

Revealing the microscopic using underwater robotic sensors

Dr. Christina Preston, Monterey Bay Aquarium Research Institute
Moss Landing Marine Labs Seminar series - November 30th, 2017

Hosted by the Environmental Biotechnology Lab

MLML Seminar Room, 4pm

Open to the public

Chris Preston received her undergraduate degree at James Madison University, PhD at UC Santa Barbara with Ed Delong, and was a Post Doc at Hopkins Marine Station with Dave Epel.  Her early work was mainly describing symbiotic associations between marine invertebrates and bacteria/archaea.  Since joining MBARI over 15 years ago, her focus has shifted more towards studying microbial populations (free-living & particle attached) throughout the water column using in situ instrumentation.

Revealing the microscopic using underwater robotic sensors

One of the long-standing challenges common to studying microorganisms in the environment is acquiring and processing samples.  Traditionally, this has involved shipboard sample collection and laboratory-based analysis.  New in situ sensors combine novel engineering and molecular biological methods and can function underwater longer than the length of research cruises.  This allows scientists to monitor and experiment within the environment in a whole new way.  In this talk, I’ll discuss how the Environmental Sample Processor (ESP) developed by MBARI can address the challenge of sample collection and processing over an extended period under non-traditional laboratory conditions, and its capability to support a variety of downstream molecular detection systems.  I’ll focus on lessons learned from the operation of our 2nd generation ESP, and how that has impacted development of our 3rd generation instrument.

Watch Dr. Preston’s MLML seminar presentation below:

Marine Heat Wave Impacts Bull Kelp Forest Ecosystems in Northern California

Dr. Laura Rogers-Bennett, UC Davis Bodega Marine Lab
Moss Landing Marine Labs Seminar Series - November 16, 2017

Hosted by the Fisheries and Conservation Biology Lab

MLML Seminar Room, 4pm

Open to the public

Dr. Laura Rogers-Bennett completed her Ph.D. in Ecology at the University of California, Davis and two post-doctoral fellowships one at U.C. Santa Cruz’s, Institute of Marine Science and the other at the U. Washington’s, Friday Harbor Labs. Dr. Rogers-Bennett is a Senior Environmental Scientist with the California Department of Fish and Wildlife in the Marine Region working at the U.C. Bodega Marine Lab. The work in her lab focuses on marine invertebrate population dynamics, fishery management and marine conservation. In the lab they use an interdisciplinary approach combining field, laboratory and quantitative modeling to examine questions related to recruitment dynamics, MPAs, marine conservation biology, fisheries sustainability, ecosystem tipping points and climate change.

Watch Dr. Rogers-Bennett’s MLML seminar presentation below:

Thesis Defense by Devona Yates- December 8th, 2017

Spatial Variation of Invertebrate Survival in Central California Kelp Forests

A Thesis Defense by Devona Yates

Ichthyology Lab

December 8th, 2017

MLML Seminar Room


Devona graduated from the University of California Santa Cruz (UCSC) in 2008 with a B.S. in Marine Biology. Before coming to Moss Landing Marine Laboratories in 2012, Devona spent four years as a scientific diver for the Partnership for Interdisciplinary Studies of Coastal Oceans (PISCO) at University of California Santa Cruz, a long-term ecosystem research and monitoring program whichconducts research in nearshore oceanography, ecological interactions, population replenishment (recruitment), population genetics, and the diversity and structure of ecological communities in central-northern California kelp forests. As an undergraduate, Devona was an assistant research diver under the supervision of PhD candidate Jan Freiwald and Dr. Mark H. Carr (UCSC), where she used acoustic telemetry and SCUBA surveys to study the movement and homerange size of temperate reef fishes, and aided in the development of microsatellite markers for a parentage analysis on adult kelp greenling (Hexagrammos decagrammus)1. Devona’s extensive amount of time spent underwater observing kelp forest organisms and their natural habitats with PISCO (over 600 coldwater dives), combined with her interest in population and community ecology led her focus of her Masters thesis on predator- prey interactions and the cascading effects of fish predation on lower trophic level organisms. This research will use tethering experiments and underwater habitat surveys in order to quantify mortality rates of invertebrate prey as a function of MPA protection status and habitat type along the Monterey Peninsula.


Thesis Abstract:

Human induced shifts in predator abundances are well documented in ecosystems all over the globe, yet the extent to which predators regulate prey populations in marine ecosystems is not fully understood. Marine reserves, a type of no-take Marine Protected Area, are effective at allowing fish populations to reestablish inside their boundaries. Since individuals targeted by fishing tend to be larger and occur at higher trophic levels, the establishment of marine reserves often results in an increase in predatory fish, and the potential to impact populations of their prey via consumptive and non-consumptive effects. In 2007, several new reserves were added to two existing marine reserves (30+ years protection) in central California, creating a network of marine reserves that prohibiting fishing. Knowledge on the recovery of predatory fishes inside these reserves and their potential effects on invertebrate prey are not well understood. By conducting field surveys and empirical predation assays (i.e., tethering experiments) inside and outside of marine reserves, I provide new evidence detailing the direct and indirect effects of changes in predator abundance for kelp forest communities. Densities of invertebrate predator fishes (i.e., invertivores) were 1.5x higher and biomass was 2.8x greater inside no-take marine reserves compared to nearby areas open to fishing. The increased abundance of predators translated to a significant reduction in survivorship of two species of decapod crustaceans, the coonstripe or dock shrimp, Pandalus danae, and the cryptic kelp crab, Pugettia richii. Shrimp mortality rates were 4.6x higher, while crab mortality rates were 7x greater inside reserves. Video analyses indicated that predatory fishes were more numerous (fmax) in the video footage and arrived sooner (tinst) to tethering arrays in reserve sites. Major shrimp predators inside reserves were Hexagrammos decagrammus (31%), Embiotoca lateralis (16%), Scorpaenichthys marmoratus (10%), and small sculpins in the family Cottidae (9%). Strike rates per hour were similar across sites, except strike rates by small sculpins, which were 14x greater inside reserves than outside. The majority (71.5%) of predation events on crabs were attributed to Octopus rubescens, based on analysis of the remains of the carapace following predation events.  Results from this research demonstrate that the removal of predatory fishes via fishing has profound effects on invertebrate populations, and may be affecting other populations of organisms within the surrounding community.


MLML’s Dr. Graham & Dr. Hamilton win a highly competitive federal funding award

Dr. Mike Graham and Dr. Scott Hamilton have been awarded a grant with California Sea Grant to research sustainable aquaculture techniques integrating seaweeds and shellfish here at Moss Landing Marine Laboratories.  The grant is one of 32 from the National Oceanic and Atmospheric Administration National Sea Grant Program

Read more on this award as announced by California Sea Grant and in an article in the Monterey Herald.

Aquaponics research at Humboldt State University

Dr. Rafael Cuevas Uribe, Humboldt State University
Moss Landing Marine Labs Seminar series - November 9, 2017

Hosted by the Phycology Lab

MLML Seminar Room, 4pm

Open to the public

Dr. Rafael Cuevas Uribe is an Assistant Professor for the Department of Fisheries Biology at Humbolt State University.  He received a PhD in Wildlife and Fisheries from Louisiana State University, a MS in Aquaculture/Aquatic Science from Kentucky State University, and a BS in Biology from Universidad de Guadalajara.

Watch Dr. Cuevas-Uribe’s MLML seminar presentation below: