Successfully Applying Species-Habitat Information toward Improving Management Decisions (hosted by AFS)

A more complete understanding of the habitat requirements of targeted and protected species is essential when developing holistic management measures to ensure their sustainability. Efforts to incorporate habitat considerations into fisheries stock assessments, species conservation measures, and resulting management decisions are dependent on fundamental habitat information throughout a species life history. As a result of improved understanding of habitat-dependent factors influencing their distribution, abundance, growth, maturity, and productivity, more accurate species abundance estimates, fishing quotas, conservation approaches, and delineations of critical and essential fish habitat have resulted. While baseline information is still needed for many species, in certain cases habitat information has been incorporated successfully into management measures and has resulted in a more comprehensive assessment. These assessments are essential for the conservation and management of living aquatic resources. Additionally these successes support ongoing efforts to incorporate differential habitat effects, vulnerabilities, and dynamics into broader management strategies under changing environments. We invite participants to share case studies regarding the successful incorporation of aquatic habitat information in the development and refining of marine, estuarine, and freshwater species management actions. Additionally, this symposium will focus on advances in research methods and tools to improve habitat information for use by decision-makers when implementing habitat-dependent management strategies.

8:00AM The Effect of a Large-Scale Stream Restoration Effort on Chinook Salmon in the Pahsimeroi River, Idaho
  Timothy Copeland, Demitra Blythe, Windy Schoby, Eli Felts, Patrick D. Murphy
Habitat restoration is an important management tool in lotic systems impaired by human activities. Although small-scale benefits of restoration are commonly investigated, it has proven difficult to demonstrate population-level effects. The Pahsimeroi River spring/summer Chinook Salmon population was previously restricted to the lower portion of the river by multiple structures. To address fish passage issues, a combination of projects was initiated including barrier removals, instream flow enhancements, and installation of diversion screens. The largest barrier was removed in 2009, approximately doubling the amount of available linear habitat. We hypothesized restoration efforts would expand the distribution of spawning Chinook Salmon in the Pahsimeroi River watershed. We also hypothesized a broader juvenile distribution would have population-level effects by reducing the prevalence of density-dependent growth and survival. Redds were documented in newly accessible habitat immediately following restoration and accounted for 25% – 57% of all redds in the watershed from 2009-2015. Snorkel surveys documented juvenile rearing in newly accessible habitat. Juvenile productivity increased from 64 smolts/female spawner pre-restoration to 99 smolts/female spawner. Increased habitat availability in the Pahsimeroi River broadened the distribution of spawning adult and rearing juvenile Chinook Salmon and reduced the effects of density-dependent survival.
8:20AM Investigating the Relationship between Habitat Type and Abundance of Micropterus Species in Two Dammed Midwestern Rivers
  Reuben Frey, Cassi Moody-Carpenter, Trent Thomas, Shannon Smith, Ryan Hastings, Robert E. Colombo
Man-made dams may affect the abundance of a fish species in lotic systems via altering flow regime and available physical habitat. Removal of dams may mitigate these effects and invite a change in species abundance. We investigated how populations of Smallmouth Bass (Micropterus dolomieu) in two Midwestern rivers were affected by the presence of low-head dam structures. Data were collected during fall and spring from 2012 to 2015 using multiple gear types at six study sites on each river; two within the below-dam reach, two within the impounded reach, and two within the run-of-river reach. Catch per unit effort (CPUE) was used to estimate fish abundance within each study site. Smallmouth Bass CPUEs differed significantly between site types during spring sampling events in both the North Fork (P= 0.02) and the Vermilion River (P= 0.03). Smallmouth Bass abundance did not differ significantly between sites in either river during fall sampling. Variation in fish abundance may be driven by physical habitat requirements along a spatial and temporal scale. Future research will investigate the effect of dam removal on changes in available physical habitat, and on the seasonal abundance of Smallmouth Bass across study sites.
8:40AM Evaluation of Environmental Conditions As Predictors for Mako Shark CPUE Using Generalized Linear Modeling and Quantile Regression to Produce Habitat Suitability Maps
  Halie OFarrell, Elizabeth Babcock
Environmental conditions were evaluated for their influence on catch per unit effort (CPUE) of shortfin mako sharks (Isurus oxyrinchus). Standardized CPUEs were calculated from the US pelagic longline observer program (1992-2016) using a generalized linear model (GLM) with a delta-lognormal approach with and without smoothers (GAM) applied to the environmental variables. Sea surface height, sea surface temperature, and bathymetry were used as predictors, resulting in an index and seasonal maps spanning 2003-2012. Sea surface temperature and bathymetry were retained in the AIC-best model to predict proportion of positive sets while bathymetry was retained to predict positive catch CPUE. Quantile regression (QR) was performed to evaluate whether environmental variables can predict spatial areas with high CPUE. The results of the GLM, GAM, and QR methods were assessed for their ability to generate habitat suitability maps. Comparison showed that QR is potentially more informative than the GLM for determining mako distribution and spatial densities. QR was performed by sex and life stage to determine the CPUE and produce habitat suitability maps that will be used to parameterize a two-dimensional individual-based model. This will be the operating model in a management strategy evaluation incorporating movement and seasonal habitat use into the management process.
9:00AM Effects of Flow Augmentation on Coho Salmon Smolt Passage and Juvenile Rearing Conditions in Porter Creek, a Tributary to the Russian River, California.
  William Boucher, Mariska Obedzinski, Zac Reinstein
Life cycle monitoring of endangered Coho Salmon (Oncorhynchus kisutch) in the Russian River has identified low summer flows and early spring disconnections as key bottlenecks to salmon recovery. In low water years, many tributaries to the Russian River, including Porter Creek, disconnect during peak smolt emigration and extensive stream drying limits survival of rearing juveniles. In collaboration with multiple organizations and a private vineyard, we developed a study to examine the effects of streamflow augmentation from an off-channel retention pond on smolt passage and juvenile rearing conditions. Streamflow gaging, PIT tag detection systems and habitat monitoring are used to monitor the effects of the augmentation at different flow release levels. In 2018, we estimate that 25% of the annual smolt run was provided passage as a result of flow releases. In 2019, we will continue to test spring flow releases to improve smolt passage and expand our study to include evaluation of the effects of augmentation on summer stream conditions in relation to survival, growth, and movement. Results will inform a flow augmentation plan that will provide guidance as to the timing, quantity and duration of releases that will most benefit fish populations in Porter Creek.
9:20AM Assessment of Offshore Sand Dredging Impacts to Essential Fish Habitat
  Deena Hansen, Bradley Pickens, J. Christopher Taylor, Mark A. Finkbeiner, Alexa Ramirez, Elizabeth Rogers, Lora Turner
Multiple uses of the Outer Continental Shelf increase pressure on fish habitat. Sand dredging for beach nourishment and coastal restoration often targets shoals, which usually function as Essential Fish Habitat (EFH) for federally managed species. In managing offshore sand dredging projects, then, the Bureau of Ocean Energy Management (BOEM) must consult with the National Marine Fisheries Service (NMFS) according to the Magnuson-Stevens Act to assess and mitigate impacts. BOEM is improving these consultations by classifying shoal features, better understanding fish-habitat associations, assessing the distribution of select fish species, and streamlining the assessment process. Shoal features were classified according to a nested scheme including shoal types, substrate, and various descriptors compatible with the Coastal and Marine Ecological Classification Standard (CMECS). In addition to EFH descriptions, fish-habitat relationships and spatial distribution were modeled using monitoring data for representative species (e.g., demersal, pelagic, shark, and reef-associated species). Resulting maps further highlight fish associations with sand features and environmental variables. To support consultations, a map-based tool including an automated template and relevant graphics improves the consistency and accuracy of BOEM’s written EFH Assessments. As ocean uses continue to expand, a better understanding of impacts, and improved communication, are integral to successful marine resource management.
09:40AM Break
10:10AM Paired Artificial-Natural Reef Studies Can Improve Our Understanding of How Artificial Structures Function As a Management Tool
  Christopher D. Stallings
Understanding the influence of habitat on populations and communities is a central goal to both ecological studies based on first principles and those that seek to inform resource management. Artificial reefs are commonly deployed in US state and federal waters to address a variety of management goals, but we often lack an understanding of how these structures function relative to natural reefs. Paired artificial-natural reefs provide a quasi-experimental system in which to improve our understanding. I will present a synthesis of recent and ongoing research on paired artificial-natural reefs in the eastern Gulf of Mexico including: 1) a comparison of population dynamics of reef fishes on these habitats, 2) why the types of artificial structures and locations where we place them may be important, 3) how fishing intensity differs between the habitats and whether such patterns are reflected in the densities and size structures of targeted fishes, and 4) production of managed species on the two habitats. I will highlight important gaps in our understanding of how they operate in complex socio-ecological systems and will provide suggestions for how future deployments may be conducted to help address these gaps and understand the role of artificial structures as a management tool.
10:30AM Importance of Oyster Reef Design and Setting in Restoration Success in Mobile Bay
  Merritt McCall, Sean Powers
Oyster reefs support an important commercial fishery as well as provide estuarine ecological services such as filtration, creation of refugia, and provision of feeding habitat for mobile and sessile species across a spectrum of life stages. Consequently, there have been increased efforts to restore and enhance the oyster reef environment in the Mobile Bay area of Alabama. A field project initiated in January 2004 was designed to determine the impact of reef design and placement along a bio-physical gradient on Eastern Oyster (Crassostrea virginica) and sessile invertebrate recruitment. Eight oyster reefs (625 m2 each), divided into four high relief (1.0 m vertical relief) and four low relief (0.1-0.2 m vertical relief), were deployed in three different areas of Mobile Bay (Cedar Point, Sand Reef, Shellbank), each varying in water quality and presence of existing oyster reefs. Initial semiannual quadrat surveys showed that recruitment and abundance of C. virginica varied with location (Cedar Point > Sand Reef > Shellbank) and reef type (high relief > low relief). Fifteen years after reef deployment, preliminary findings suggest persistence of the established bio-physical gradient of C. virginica abundance. Understanding the extent of the success of this restoration design will help inform future restoration decisions.
10:50AM Gray Snapper (Lutjanus griseus) Distribution and Abundance in the Alabama Artificial Reef Zone
  Edward Kim, Sean Powers
Gray Snapper (Lutjanus griseus) constitute a significant recreational and minor commercial fishery throughout the Gulf of Mexico (GOM) and have been hypothesized to increase in abundance in several states as a result of predicted global warming. A 2018 assessment by the Southeast Data, Assessment, and Review (SEDAR) determined that the stock is not currently overfished nor undergoing overfishing. However, spatiotemporal gaps in our understanding of the habitat requirements for these fish that could better inform fishery management exist, particularly within Alabama waters. This study aims to address the distribution and abundance of the Gray Snapper population through the analysis of remotely operated vehicle (ROV) footage taken in the 1000 km2 Alabama Artificial Reef Zone (AARZ) from 2011-2018. Min count data from these videos will be used to generate a standardized index of relative abundance to evaluate the significance of environmental explanatory factors. Results will elucidate habitat preferences across different artificial and natural structures as well as estimate abundance on these structures throughout the spatial coverage of the AARZ. These findings will also introduce new data for future stock assessments as the stock potentially expands.
11:10AM Go West (and South) Young Smelt: Mapping the Habitats Associated with Juvenile Longfin Smelt and Testing Our Predictions
  Corey Phillis, Dave Fullerton, Aaron Bever, Michael MacWilliams, John Brandon, Lenny Grimaldo
Management and conservation of listed species requires an understanding of the environmental characteristics associated with species distribution. Previous research in the San Francisco Estuary has emphasized the importance of spring freshwater outflow to support the state-listed Longfin Smelt (LFS) population. However, in wet years the index of juvenile LFS declines because the population distributes downstream of the California Department of Fish Wildlife (CDFW) 20-mm survey stations. To improve our understanding of factors associated with juvenile LFS distribution, we examined two decades of LFS catch data using Boosted Regression Tree analysis. Turbidity, conductivity, and temperature dominated the relative importance of predictor variables, consistent with other studies of LFS catch. Mapping predicted catch of juvenile LFS throughout the entire San Francisco Estuary consistently identified habitats associated with LFS presence downstream of the CDFW 20-mm survey footprint, particularly in wet years. We tested the model predictions by sampling habitats associated with juvenile LFS catch in areas currently not sampled by the CDFW 20-mm survey. Our results provide managers with an improved understanding of the habitats associated with juvenile Longfin Smelt and identify new regions within the San Francisco Estuary where management may benefit the conservation and recovery of this state-listed species.

Organizers: Tony Marshak, Margaret (Peg) Brady
Supported by: AFS Fish Habitat Section

Location: Reno-Sparks CC Date: October 2, 2019 Time: 8:00 am - 11:50 am