Christopher M. Holbrook

Survival of Migrating Atlantic Salmon Smolts through the Penobscot River, Maine: a Prerestoration Assessment

Abstract Survival, distribution, and behavior of hatchery (n = 493) and naturally reared (n = 133) smolts of Atlantic salmon Salmo salar migrating through the Penobscot River and estuary in Maine were evaluated with acoustic telemetry in 2005 and 2006. Survival and use of a secondary migration path (the Stillwater Branch) were estimated with a multistate mark–recapture model. Higher rates of mortality per kilometer (range = 0.01–0.22) were observed near release sites and within reaches that contained three particular dams: Howland, West Enfield, and Milford dams. Estimated total survival of tagged hatchery smolts through entire individual reaches containing those dams ranged from 0.52 ( 0.18) to 0.94 ( 0.09), whereas survival through most of the reaches without dams exceeded 0.95. Of those smolts that survived to the Penobscot River–Stillwater Branch split at Marsh Island, most (≥74%) remained in the main stem around Marsh Island, where they experienced lower survival than fish that used the Stillwater Br...

Acoustic telemetry and fisheries management

This paper reviews the use of acoustic telemetry as a tool for addressing issues in fisheries management, and serves as the lead to the special Feature Issue of Ecological Applications titled Acoustic Telemetry and Fisheries Management. Specifically, we provide an overview of the ways in which acoustic telemetry can be used to inform issues central to the ecology, conservation, and management of exploited and/or imperiled fish species. Despite great strides in this area in recent years, there are comparatively few examples where data have been applied directly to influence fisheries management and policy. We review the literature on this issue, identify the strengths and weaknesses of work done to date, and highlight knowledge gaps and difficulties in applying empirical fish telemetry studies to fisheries policy and practice. We then highlight the key areas of management and policy addressed, as well as the challenges that needed to be overcome to do this. We conclude with a set of recommendations about how researchers can, in consultation with stock assessment scientists and managers, formulate testable scientific questions to address and design future studies to generate data that can be used in a meaningful way by fisheries management and conservation practitioners. We also urge the involvement of relevant stakeholders (managers, fishers, conservation societies, etc.) early on in the process (i.e., in the co-creation of research projects), so that all priority questions and issues can be addressed effectively.

Toward a national animal telemetry network for aquatic observations in the United States

Animal telemetry is the science of elucidating the movements and behavior of animals in relation to their environment or habitat. Here, we focus on telemetry of aquatic species (marine mammals, sharks, fish, sea birds and turtles) and so are concerned with animal movements and behavior as they move through and above the world’s oceans, coastal rivers, estuaries and great lakes. Animal telemetry devices (“tags”) yield detailed data regarding animal responses to the coupled ocean–atmosphere and physical environment through which they are moving. Animal telemetry has matured and we describe a developing US Animal Telemetry Network (ATN) observing system that monitors aquatic life on a range of temporal and spatial scales that will yield both short- and long-term benefits, fill oceanographic observing and knowledge gaps and advance many of the U.S. National Ocean Policy Priority Objectives. ATN has the potential to create a huge impact for the ocean observing activities undertaken by the U.S. Integrated Ocean Observing System (IOOS) and become a model for establishing additional national-level telemetry networks worldwide.BackgroundTelemetry can provide environmental, behavioral and physiological data in near-real time, or by use of archival tags in which the data are stored or later transmitted to satellites. Aquatic animal species tagged have ranged from 6-g salmon smolts to 150-ton whales. Detailed observations of animal movements and behavior in relation to critical habitats in their aquatic environment have significantly improved our understanding of ecosystem function and dynamics. These observations are critical for sustaining populations, conserving biodiversity and implementing ecosystem-based management through an increased understanding of ecosystem structures, functions, and processes, as well as their importance to ecosystem services and values. Sensors carried by tagged animals have come of age and deliver high-resolution physical oceanographic data at relatively low costs. Animals are particularly adept at helping scientists identify critical habitats, spawning locations, and important oceanographic features (e.g., fronts, eddies and upwelling areas). They also provide important insights into regions of the oceans that are difficult and expensive to monitor (e.g., offshore environments, Arctic). This paper focuses on how to integrate an operational ATN into U.S. IOOS.ResultsThe development of U.S. IOOS initially focused on the acquisition and integration of physical and chemical oceanographic data. With this system now operational, U.S. IOOS is ready to add the acquisition of relevant biological observations, and to enhance the acquisition of physical and chemical oceanographic observations via ATN platforms.ConclusionA U.S. ATN observing system that monitors aquatic life on a range of temporal and spatial scales could yield both short- and long-term benefits, fill oceanographic observing and knowledge gaps, and advance many of the National Ocean Policy Priority Objectives. ATN has the potential to create a huge impact for the ocean observing activities undertaken by IOOS and become a model for establishing additional national-level telemetry networks worldwide.

Spatial and temporal variation in positioning probability of acoustic telemetry arrays: fine-scale variability and complex interactions

AbstractBackgroundnAs popularity of positional acoustic telemetry systems increases, so does the need to better understand how they perform in real-world applications, where variation in performance can bias study conclusions. Studies assessing variability in positional telemetry system performance have focused primarily on position accuracy, or comparing performance inside and outside the array. Here, we explored spatial and temporal variation in positioning probability within a 140-receiver Vemco Positioning System (VPS) array used to monitor lake trout, Salvelinus namaycush, spawning behavior over 23xa0km2 in Lake Huron, North America.MethodsVariability in VPS positioning probability was assessed between August and November from 2012 to 2014 using 43 stationary transmitters distributed throughout the array. Various analyses were used to relate positioning probability to number of fish transmitters in the array, wave height, and thermal stratification. We also assessed the prevalence of ‘close proximity detection interference’ (CPDI) in our array by analyzing detection probability of 35 transmitters on collocated receivers.ResultsPositioning probability of the VPS array varied greatly over time and space. Number of fish transmitters present in the array was a significant driver of reduced positioning probability, especially during lake trout spawning period when the fish were aggregated. Relationships between positioning probability and environmental variables were complex and varied over small spatial and temporal scales. One possible confounding variable was the large range of water depth over which receivers were deployed. Another confounding factor was the high prevalence of CPDI, which decreased exponentially with water depth and was less evident when wave heights were higher than normal.ConclusionsSome variables that negatively influenced positioning can be minimized through careful planning (e.g., number of tagged fish released, transmitter power level). However, results suggested that the acoustic environment was highly variable over small spatial and temporal scales in response to complex interactions between many variables. Therefore, models that predict positioning or detection efficiencies as a function of environmental variables may not be attainable in most systems. The best defense against biased study conclusions is incorporation of in situ measures of system performance that allow for retrospective analysis of array performance after a study is completed.

Fine-Scale Pathways Used By Adult Sea Lampreys during Riverine Spawning Migrations

AbstractBetter knowledge of upstream migratory patterns of spawning Sea Lampreys Petromyzon marinus, an invasive species in the Great Lakes, is needed to improve trapping for population control and assessment. Although trapping of adult Sea Lampreys provides the basis for estimates of lake-wide abundance that are used to evaluate the Sea Lamprey control program, traps have only been operated at dams due to insufficient knowledge of Sea Lamprey behavior in unobstructed channels. Acoustic telemetry and radiotelemetry were used to obtain movement tracks for 23 Sea Lampreys in 2008 and 18 Sea Lampreys in 2009 at two locations in the Mississagi River, Ontario. Cabled hydrophone arrays provided two-dimensional geographic positions from acoustic transmitters at 3-s intervals; depth-encoded radio tag detections provided depths. Upstream movements occurred at dusk or during the night (2015–0318xa0hours). Sea Lampreys were closely associated with the river bottom and showed some preference to move near banks in shall...

Effects of acoustic tag implantation on lake sturgeon Acipenser fulvescens: lack of evidence for changes in behavior

BackgroundAn assumption of studies using acoustic telemetry is that surgical implantation of acoustic transmitters or tags does not alter behavior of tagged individuals. Evaluating the validity of this assumption can be difficult for large fish, such as adult sturgeons, not amenable to controlled laboratory experimentation. The purpose of this study was to determine if and when this assumption was valid for adult lake sturgeon Acipenser fulvescens tagged with large (34xa0g) acoustic transmitters and released into the St. Clair River during 2011–2014. The hypothesis that activity and reach-scale distributions of tagged and untagged lake sturgeon did not differ was tested by comparing movement frequencies, movement rates (speed-over-ground), and location-specific detection probabilities between newly-tagged lake sturgeon and presumably fully-recovered conspecifics tagged and released in prior years.ResultsActivity of acoustic-tagged lake sturgeon did not differ between newly-tagged individuals and conspecifics tagged in prior years. Movement frequencies and movement rates in all comparisons were similar between lake sturgeon observed during the first 15xa0days after surgery and simultaneously-observed conspecifics tagged in prior years. Likewise, lake sturgeon observed during the first 15xa0days after release were not more likely than conspecifics tagged in prior years to be distributed upstream or downstream of release sites. However, newly-tagged lake sturgeon were more likely than conspecifics tagged in prior years to be detected near release areas. Whether the cause for this ephemeral difference in detection probabilities was a behavioral response to surgery or a consequence of releasing newly-tagged individuals near receivers could not be determined.ConclusionsLack of evidence for changes in movement frequencies, movement rates, and distribution after surgical implantation of acoustic tags supported the assumption that movements of acoustic-tagged adult lake sturgeon were representative of untagged conspecifics. Thus, detection data gathered from recently tagged individuals is unlikely to bias data analyses in studies of lake sturgeon spatial ecology using telemetry. Our findings should apply to most tag sizes given that we used some of the largest acoustic tags currently available. The “staggered entry” design used in this study also may be useful for testing fundamental assumptions of biotelemetry studies for other large fish.

Probability of acoustic transmitter detections by receiver lines in Lake Huron: results of multi-year field tests and simulations

BackgroundAdvances in acoustic telemetry technology have led to an improved understanding of the spatial ecology of many freshwater and marine fish species. Understanding the performance of acoustic receivers is necessary to distinguish between tagged fish that may have been present but not detected and from those fish that were absent from the area. In this study, two stationary acoustic transmitters were deployed 250xa0m apart within each of four acoustic receiver lines each containing at least 10 receivers (i.e., eight acoustic transmitters) located in Saginaw Bay and central Lake Huron for nearly 2xa0years to determine whether the probability of detecting an acoustic transmission varied as a function of time (i.e., season), location, and distance between acoustic transmitter and receiver. Distances between acoustic transmitters and receivers ranged from 200xa0m to >10xa0km in each line. The daily observed probability of detecting an acoustic transmission was used in simulation models to estimate the probability of detecting a moving acoustic transmitter on a line of receivers.ResultsThe probability of detecting an acoustic transmitter on a receiver 1000xa0m away differed by month for different receiver lines in Lake Huron and Saginaw Bay but was similar for paired acoustic transmitters deployed 250xa0m apart within the same line. Mean probability of detecting an acoustic transmitter at 1000xa0m calculated over the study period varied among acoustic transmitters 250xa0m apart within a line and differed among receiver lines in Lake Huron and Saginaw Bay. The simulated probability of detecting a moving acoustic transmitter on a receiver line was characterized by short periods of time with decreased detection. Although increased receiver spacing and higher fish movement rates decreased simulated detection probability, the location of the simulated receiver line in Lake Huron had the strongest effect on simulated detection probability.ConclusionsPerformance of receiver lines in Lake Huron varied across a range of spatiotemporal scales and was inconsistent among receiver lines. Our simulations indicated that if 69xa0kHz acoustic transmitters operating at 158xa0dB in 10–30xa0m of freshwater were being used, then receivers should be placed 1000xa0m apart to ensure that all fish moving at 1xa0mxa0s−1 or less will be detected 90% of days over a 2-year period. Whereas these results can be used as general guidelines for designing new studies, the irregular variation in acoustic transmitter detection probabilities we observed among receiver line locations in Lake Huron makes designing receiver lines in similar systems challenging and emphasizes the need to conduct post hoc analyses of acoustic transmitter detection probabilities.

Divergent migration within lake sturgeon (Acipenser fulvescens) populations: Multiple distinct patterns exist across an unrestricted migration corridor

Population structure, distribution, abundance and dispersal arguably underpin the entire field of animal ecology, with consequences for regional species persistence, and provision of ecosystem services. Divergent migration behaviours among individuals or among populations are an important aspect of the ecology of highly mobile animals, allowing populations to exploit spatially or temporally distributed food and space resources. This study investigated the spatial ecology of lake sturgeon (Acipenser fulvescens) within the barrier free Huron-Erie Corridor (HEC), which connects Lake Huron and Lake Erie of the North American Laurentian Great Lakes. Over 6xa0years (2011-2016), movements of 268 lake sturgeon in the HEC were continuously monitored across the Great Lakes using acoustic telemetry (10xa0years battery life acoustic transmitters). Five distinct migration behaviours were identified with hierarchical cluster analysis, based on the phenology and duration of river and lake use. Lake sturgeon in the HEC were found to contain a high level of intraspecific divergent migration, including partial migration with the existence of residents. Specific behaviours included year-round river residency and multiple lake-migrant behaviours that involved movements between lakes and rivers. Over 85% of individuals were assigned to migration behaviours as movements were consistently repeated over the study, which suggested migration behaviours were consistent and persistent in lake sturgeon. Differential use of specific rivers or lakes by acoustic-tagged lake sturgeon further subdivided individuals into 14 contingents (spatiotemporally segregated subgroups). Contingents associated with one river (Detroit or St. Clair) were rarely detected in the other river, which confirmed that lake sturgeon in the Detroit and St. Clair represent two semi-independent populations that could require separate management consideration for their conservation. The distribution of migration behaviours did not vary between populations, sexes, body size or among release locations, which indicated that intrapopulation variability in migratory behaviour is a general feature of the spatial ecology of lake sturgeon in unfragmented landscapes.

Relative performance of three stream bed stability indices as indicators of stream health

Bed stability is an important stream habitat attribute because it affects geomorphology and biotic communities. Natural resource managers desire indices of bed stability that can be used under a wide range of geomorphic conditions, are biologically meaningful, and are easily incorporated into sampling protocols. To eliminate potential bias due to presence of instream wood and increase precision of stability values, we modified a stream bed instability index (ISI) to include measurements of bankfull depth (dbf) and median particle diameter (D50) only in riffles and increased the pebble count to decrease variability (i.e., increase precision) in D50. The new riffle-based instability index (RISI) was compared to two established indices: ISI and the riffle stability index (RSI). RISI and ISI were strongly associated with each other but neither was closely associated with RSI. RISI and ISI were closely associated with both a diatom- and two macrovertebrate-based stream health indices, but RSI was only weakly associated with the macroinvertebrate indices. Unexpectedly, precision of D50 did not differ between RISI and ISI. Results suggest that RISI is a viable alternative to both ISI and RSI for evaluating bed stability in multiple stream types. With few data requirements and a simple protocol, RISI may also better conform to riffle-based sampling methods used by some water quality practitioners.

Use of navigation channels by Lake Sturgeon: Does channelization increase vulnerability of fish to ship strikes?

Channelization for navigation and flood control has altered the hydrology and bathymetry of many large rivers with unknown consequences for fish species that undergo riverine migrations. In this study, we investigated whether altered flow distributions and bathymetry associated with channelization attracted migrating Lake Sturgeon (Acipenser fulvescens) into commercial navigation channels, potentially increasing their exposure to ship strikes. To address this question, we quantified and compared Lake Sturgeon selection for navigation channels vs. alternative pathways in two multi-channel rivers differentially affected by channelization, but free of barriers to sturgeon movement. Acoustic telemetry was used to quantify Lake Sturgeon movements. Under the assumption that Lake Sturgeon navigate by following primary flow paths, acoustic-tagged Lake Sturgeon in the more-channelized lower Detroit River were expected to choose navigation channels over alternative pathways and to exhibit greater selection for navigation channels than conspecifics in the less-channelized lower St. Clair River. Consistent with these predictions, acoustic-tagged Lake Sturgeon in the more-channelized lower Detroit River selected the higher-flow and deeper navigation channels over alternative migration pathways, whereas in the less-channelized lower St. Clair River, individuals primarily used pathways alternative to navigation channels. Lake Sturgeon selection for navigation channels as migratory pathways also was significantly higher in the more-channelized lower Detroit River than in the less-channelized lower St. Clair River. We speculated that use of navigation channels over alternative pathways would increase the spatial overlap of commercial vessels and migrating Lake Sturgeon, potentially enhancing their vulnerability to ship strikes. Results of our study thus demonstrated an association between channelization and the path use of migrating Lake Sturgeon that could prove important for predicting sturgeon-vessel interactions in navigable rivers as well as for understanding how fish interact with their habitat in landscapes altered by human activity.