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Jeremy Holden

Publications and source records attributed to Jeremy Holden.

13 recordsLinked to original sources
USGS2023

Lake Ontario April prey fish survey results and Alewife assessment, 2023

The April bottom trawl survey and Alewife Alosa pseudoharengus population assessment provides science to inform Lake Ontario fisheries management. The 2023 survey included 215 trawls in the main lake and embayments, and sampled depths from 6.5 to 252 m (21-833 ft). The survey captured 1,012,178 fish from 32 species with a total weight of 12,136 kg (26,700 lbs.). Alewife were 92% of the catch by number while Rainbow Smelt, Osmerus mordax , Deepwater Sculpin, Myoxocephalus thompsonii , and Round Goby, Neogobius melanostomus , comprised 3%, 3%, and 1% of the catch, respectively. To improve the accuracy of prey fish biomass and density estimates we reanalyzed trawl sensor data from each of three participating survey vessels and created vessel-specific relationships predicting how bottom trawl bottom contact time, wing width, and area-swept varies with depth. Total Alewife biomass increased in 2023 due to growth and survival of the abundant 2020 year class (now age-3) and an abundant 2022 year class (age-1). The 2023 mean Alewife biomass (81.1 kg·ha -1 ) was the largest since whole lake sampling began in 2016 and was the ninth largest value observed in the modern time series (1997-2023, maximum value in 2000 = 91.8 kg·ha -1 ). The 2023 Alewife density (6795 n·ha -1 ) was the greatest density observed in the modern time series. These high biomass and density values are due to above average Alewife reproductive success in 2020 and 2022. Simulation modeling suggests the 2024 and 2025 Alewife biomass index may be substantially higher than the 2023 observations. In 2023, the Rainbow Smelt biomass index increased relative to the 2022 index, as did the biomass index for Cisco, Coregonus artedi . In contrast, Emerald Shiner Notropis atherinoides and Threespine Stickleback Gasterosteus aculeatus , biomass values continue to be low (< 0.01 kg·ha -1 ). Three Bloater Coregonus hoyi , were captured during the 2023 survey. Hydroacoustic sampling conducted during the bottom trawl survey estimated prey fish densities in pelagic habitats not sampled by the bottom trawl (3 m below the surface to 3 m above the lake bottom) and these densities were hundreds to thousands of times lower than bottom trawl-based densities. These results support the idea that, in April, when the warmest water is on the lake bottom, Alewife and most other pelagic prey fish are near the lake bottom and can be effectively sampled with bottom trawling.

Lake Ontario↗
USGS2022

Results of the collaborative Lake Ontario bloater restoration stocking and assessment, 2012–2020

Bloater, Coregonus hoyi , are deepwater planktivores native to the Laurentian Great Lakes and Lake Nipigon. Interpretations of commercial fishery time series suggest they were common in Lake Ontario through the early 1900s but by the 1950s were no longer captured by commercial fishers. Annual bottom trawl surveys that began in 1978 and sampled extensively across putative bloater habitat only yielded one individual (1983), suggesting that the species had been locally extirpated. In 2012, a multiagency restoration program stocked bloater into Lake Ontario from gametes collected in Lake Michigan. From 2012 to 2020, 1,028,191 bloater were stocked into Lake Ontario. Bottom trawl surveys first detected stocked fish in 2015, and through 2020 ten bloater have been caught (total length mean = 129 mm, s.d. = 44 mm, range: 96–240 mm). Hatchery applied marks and genetic analyses confirmed the species identification and identified stocking location for some individuals. Trawl capture locations and acoustic telemetry suggested that stocked fish dispersed throughout the main lake within months or sooner, and the depth distribution of recaptured bloater was similar to historic distributions in Lake Ontario and other Great Lakes. Predicted bloater trawl catches, based on modeled population abundance and trawl survey efficiency, were similar to observed catches, suggesting that post-stocking survival is less than 20% and contemporary bottom trawl surveys can quantify bloater abundance at low densities and track restoration.

Lake Ontario↗
USGS2022

Lake Ontario April prey fish survey results and Alewife assessment, 2022

The annual Lake Ontario April bottom trawl survey and Alewife, Alosa pseudoharengus , population assessment provide science to inform management decisions related to predator-prey balance and fish community dynamics. The 2022 survey was conducted from March 31 to April 26, included 235 trawls in the main lake and embayments, and sampled depths from 5 to 219 m (16 – 723 ft). The survey captured 311,770 fish from 30 species with a total weight of 7,740 kg (17,028 lbs.). Alewife were 85% of the catch by number while Rainbow Smelt, Osmerus mordax , Round Goby, Neogobius melanostomus , and Deepwater Sculpin, Myoxocephalus thompsonii , comprised 6%, 4%, and 4% of the catch, respectively. The 2022 biomass index for Rainbow Smelt decreased 80% relative to the high values observed in 2021 as did the value for Cisco, Coregonus artedi , (46% decline). Emerald Shiner, Notropis atherinoides , biomass index increased in 2021 and Threespine Stickleback, Gasterosteus aculeatus , biomass remained low. No Bloater, Coregonus hoyi , were captured during the 2022 survey. In 2022, Alewife biomass in U.S. waters (58.1 kilograms per hectare, kg·ha-1) was substantially higher than Canadian waters (26.3 kg·ha-1). The 2022 Alewife biomass index (41.6 kg·ha-1) decreased 10% from 2021 while the 2022 density index decreased 62% from 2021. Prediction modeling indicated the growth of the abundant 2020 Alewife year class, sampled as age-1 fish in 2021, would cause the adult Alewife biomass to increase in 2022. Although the adult Alewife biomass did increase relative to 2021 (61%), the increase was lower than predicted. The difference between the predictions and observations was because survival of age-1 fish from 2021 to 2022 was lower than had previously been observed. In the three previous years of observations the proportion of age-1 Alewife surviving to age 2 ranged from 0.33 to 0.53; however, that proportion was only 0.21 from 2021 to 2022. Survival estimates of Alewife age-5 through age-8 were higher than previously observed, possibly because salmonid predation focused on the abundant younger Alewife. The catch of age-1 Alewife in 2022, which is a measure of reproductive success in 2021, was below average and similar to the abundances of the 2018 and 2019 year classes. Simulation modeling results indicated the adult Alewife biomass is likely to increase slightly in 2023, whereas predictions for 2024 are less certain. Hydroacoustic sampling was used to estimate prey fish densities in open-water, pelagic habitats not sampled by the bottom trawl. Bottom trawl-based densities from the lake bottom were at least 25 times greater than densities of prey fish in the water column above the trawl. These results support the idea that, in April, when the warmest, most dense water is on the lake bottom, Alewife and most other pelagic prey fish primarily inhabit deep, near bottom habitats and can be effectively sampled with bottom trawling.

Lake Ontario↗
USGS2021

Stationary hydroacoustics demonstrates vessel avoidance biases during mobile hydroacoustic surveys of alewife in Lake Ontario

Mobile hydroacoustic surveys are routinely used to estimate pelagic fish abundance . In the Great Lakes, alewife are commonly surveyed with mobile hydroacoustics, however, their behavior often has them associated with epilimnetic habitats which increases the potential for vessel avoidance to bias hydroacoustic observations. Abundance estimates from mobile hydroacoustic surveys are typically made using depth and size thresholds to classify targets to species. In hydroacoustic surveys, fish can appear to be smaller when oriented off horizontal axis, as is common with fish displaying vessel avoidance behaviour. This presents a problem where alewives that are diving may appear too small to be correctly classified. We compared alewife swimming behaviours and target strength distributions between stationary up-looking and mobile down-looking hydroacoustics to quantify how vessel avoidance may bias hydroacoustic observations. Alewives from the mobile survey were found to be diving away from the surface, moving faster and in more linear paths than the undisturbed fish from the stationary survey. In the mobile survey, alewives were observed at smaller target strength values than would be expected if boat avoidance was not occurring. Our results suggest that alewife behavioral changes associated with vessel avoidance affect the number and size of targets classified as alewife from mobile hydroacoustic surveys in Lake Ontario.

Lake Ontario↗
USGS2021

Incorporation of non-native species in the diets of cisco (Coregonus artedi) from eastern Lake Ontario

Cisco Coregonus artedi was once an important native fish in Lake Ontario; however, after multiple population crashes, the cisco stock has yet to recover to historic abundances. Rehabilitation of cisco in Lake Ontario is a fish community management objective, but the extent to which recent non-native species and pelagic food web changes have influenced cisco is not well understood. We described cisco diets in contemporary Lake Ontario following the addition and spread of non-native zooplankton species. We collected 618 cisco and processed 178 for full diet analysis in eastern Lake Ontario using mid-water trawls and bottom-set gill nets from 2016 to 2020. We found that Lake Ontario cisco were mostly zooplanktivorous, and non-native zooplankton dominated their diet during July and September. Cisco smaller than 300 mm had a more diverse diet including both native and non-native zooplankton, while cisco larger than 300 mm fed almost exclusively on non-native predatory cladocerans Bythotrephes longimanus and Cercopagis pengoi (98.9% consumed prey dry mass). We also found fish eggs, presumed to be of coregonine origin in 75% of non-empty December-collected cisco diets, suggesting eggs subsidize cisco diets when available. Juvenile round goby Neogobius melanostomus , alewife Alosa pseudoharengus and rainbow smelt Osmerus mordax were found in 2% of all analyzed non-empty stomachs. Lake Ontario cisco diet appears to be more similar to zooplanktivorous Lake Superior cisco than Lake Michigan where piscivory is prevalent. Lake Ontario cisco diets reflected zooplankton community changes indicating that non-native predatory cladocerans are now an important energy source supporting this native species.

Eastern Lake Ontario↗
USGS2021

Lake Ontario cisco population dynamics based on long-term surveys

Prior to European settlement, cisco (Coregonus artedi) were likely one of Lake Ontario’s most abundant fishes but currently represent a small portion of the fish community. To understand how the population has changed over the past 70 years we compared trends in annual catch rates from gillnet and bottom trawl surveys and commercial fishery landings. In surveys, cisco were generally rare, and represented 0.2, 0.4, and 0.001% of all fish caught in two gillnet surveys and bottom trawl surveys. Cisco catch rates in gillnets and trawls were positively correlated and correlations increased when gillnet catches two years later were compared to trawls since trawls tended to capture smaller, juvenile-sized cisco relative to gillnets. Survey catch rates suggest recruitment is generally low, but discrete periods of relatively greater recruitment in the 1980s and mid-2010s suggest reproductive conditions for cisco vary temporally. Trawl surveys were the most spatially extensive survey and illustrated catch rates were highest in northeastern Lake Ontario. Greater cisco abundance in this region may be related to more-abundant embayment spawning habitat, greater distance from winter aggregations of nonnative planktivores, or more appropriate environmental conditions during spawing. At the basin scale, Lake Ontario bottom trawl catch per unit effort (CPUE) was positively correlated to Lake Superior trawl CPUE suggesting a regional driver, such as climate, may be similarly impacting both populations. Concurrent patterns across Lake Ontario surveys support the idea that cisco are currently a small portion of the fish community, recruitment remains inconsistent, and habitats in northeastern Lake Ontario appear critical to the remnant populations.

Lake Ontario↗
USGS2021

Lake Ontario April prey fish survey and Alewife assessment, 2021

The Lake Ontario April bottom trawl survey and Alewife, Alosa psuedoharengus population assessment are conducted annually to track prey fish community status and aid management decisions related to predator-prey balance. No survey was conducted in 2020 due to the Covid-19 pandemic. The 2021 survey included 248 bottom trawls in both U.S. and Canadian waters, from March 30 - May 7 in the main lake and embayment regions, at depths ranging from 5 – 221 m (16 - 729 ft). The survey captured 947,102 fish, from 30 species with a total weight of 9,191 kg (20,220 lbs). Alewife were 89.2% of the catch by number while Rainbow Smelt, Osmerus mordax , Round Goby Neogobius melanostomus , and Deepwater Sculpin Myoxocephalus thompsonii comprised 5.6, 2.3, and 1.7% of the catch, respectively. Rainbow Smelt biomass in 2021 was among the highest values observed since 1997, especially in U.S. waters. The biomass index for Cisco, Coregonus artedii also increased, primarily due to catches and greater survey effort in the Bay of Quinte. Threespine stickleback, Gasterosteus aculeatus and Emerald Shiner, Notropis atherinoides biomasses remain low. No Bloater, Coregonus hoyi were captured during the 2021 survey. In 2021, the lake-wide Alewife biomass index increased substantially from 2019 due to the presence of an exceptionally high catch of age-1 Alewife (2020 year class). The biomass index of adult Alewife (age-2 and up) declined slightly since 2019, which was expected since Alewife reproduction was generally below average from 2016 to 2019. Expanding the survey spatial extent from U.S. waters to a lake-wide survey in 2016 has improved our ability to estimate Alewife survival and has provided more accurate estimates of Lake Ontario Alewife biomass and density. Simulation modeling based on recent estimates of survival, growth, and reproduction suggests the adult Alewife biomass will likely increase in 2022 and 2023. As part of a continued effort to improve prey fish surveys, we employed hydroacoustic sampling during the 2021 April trawl survey to estimate fish densities in open-water, pelagic habitats not sampled by the bottom trawl. We found fish density, in waters above the trawl headline depth (3m off bottom to surface), were approximately ~100 times lower than pelagic prey fish densities from bottom trawls. These results support the idea that at this time of year, when the warmest water is on the lake bottom, Alewife and most other prey fish primarily inhabit deep, near bottom regions and can be effectively sampled with bottom trawls. We were not able to apportion acoustics targets to species, however the low mean target strength (-43 decibels, dB) suggested these were small fishes (e.g., 100 mm). The greatest hydroacoustics densities were found near the Niagara River confluence and future surveys may use midwater trawls to determine which species these were and continue to improve this multi-agency survey.

Lake Ontario↗
USGS2020

Lake Ontario deepwater sculpin recovery: An unexpected outcome of ecosystem change

Fish population recoveries can result from ecosystem change in the absence of targeted restoration actions. In Lake Ontario, native Deepwater Sculpin Myoxecephalus thompsonii, were common in the late-1800s, but by the mid-1900s the species was possibly extirpated. During this period mineral nutrient inputs increased and piscivore abundance declined, which increased the abundance of the nonnative planktivores Alewife Alosa pseudoharengus and Rainbow Smelt Osmerus mordax. Deepwater Sculpin larvae are pelagic and vulnerable to predation by planktivores. Annual bottom trawl surveys did not capture Deepwater Sculpin from 1978 – 1995 (n = 6,666 tows) despite sampling appropriate habitat (trawl depths: 7 – 170 m). The absence of observations during this time resulted in an elevated conservation status for the species, but no restoration actions were initiated. In 1996, three individuals were caught in bottom trawls, the first observed since 1972. Since then, their abundance has increased and in 2017 they were the second most abundant Lake Ontario prey fish. The food-web changes that occurred from 1970 through the 1990s contributed to this recovery. Alewife and Rainbow Smelt abundance declined during this period due to predation by stocked salmonids and legislation that reduced nutrient inputs and food web productivity. In the 1990s, the proliferation of nonnative, filter-feeding dreissenid mussels dramatically increased water clarity. As light penetration increased, the early-spring depth distribution of Alewife and Rainbow Smelt shifted deeper, away from larval Deepwater Sculpin habitat. The intentional and unintentional changes that occurred in Lake Ontario were not targeted at Deepwater Sculpin restoration but resulted in conditions that favored the species’ recovery. While standard surveys documented the recovery, more diverse information (e.g. observations in deep habitats and early-life stages) would have improved our understanding of why the species recovered when it did. Annual Lake Ontario trawl surveys have collaboratively expanded their spatial extent and diversified habitat sampled, based on lessons learned from the Deepwater Sculpin recovery.

Lake Ontario↗
USGS2019

Bottom trawl assessment of Lake Ontario prey fishes

Collaborative Lake Ontario bottom trawl surveys, led by the United States Geological Survey (USGS), provide science and management information for evaluating Fish Community Objectives including predator-prey balance and prey fish community diversity. In 2018, the New York State Department of Environmental Conservation (NYSDEC), Ontario Ministry of Natural Resources and Forestry (OMNR), and the (USGS) completed an April bottom trawl survey (n = 208 tows) and an October survey (n = 118 tows), at depths 6-228 m, and captured 384,651 fish from 31 species. Alewife were 80% of the total catch by number and round goby, deepwater sculpin, and rainbow smelt comprised 12, 4, and 3% of the catch, respectively. The adult alewife abundance index for U.S. waters decreased in 2018 relative to 2017, while the index in Canadian waters increased. While lake wide density increased, biomass indices for Age-2 alewife decreased. Alewife condition indices were below the 10-year average for both the April and October indices. The 2018 Age-1 alewife abundance index, which measures reproductive success the previous year, was the third lowest observed in U.S. waters over the past 22 years. The Canadian Age-1 index 2018 value was four-times larger than the U.S. value. Within-year differences between Canadian and U.S. alewife abundance indices, highlight the importance of assessing Lake Ontario fishes at a whole-lake scale. Abundance indices for rainbow smelt, threespine stickleback and emerald shiner were similar to 2017. New experimental trawl sites in embayment habitats generally captured more species, a higher proportion of native species, and higher densities relative to similar depth sites in the main lake and regions adjacent to embayments. Pelagic prey fish diversity continues to be low because a single species, alewife, dominates the catch. Deepwater sculpin and round goby were the most abundant demersal (bottom-oriented) prey fishes in 2018. Slimy sculpin and native nearshore demersal prey fishes, which were historically more abundant in trawl catches, are rare and restricted to specific habitats, since round goby proliferation. Despite declines in some species, demersal prey fish community diversity continues to increase as deepwater sculpin and round goby comprise more even portions of the community in contrast to when a single species, slimy sculpin, dominated the community. Five bloater were captured in the 2018 surveys which is the largest number captured in Lake Ontario since restoration stocking began in 2012.

Lake Ontario↗
USGS2018

Bottom trawl assessment of Lake Ontario prey fishes

Managing Lake Ontario fisheries in an ecosystem-context requires prey fish community and population data. Since 1978, multiple annual bottom trawl surveys have quantified prey fish dynamics to inform management relative to published Fish Community Objectives. In 2017, two whole-lake surveys collected 341 bottom trawls (spring: 204, fall: 137), at depths from 8-225m, and captured 751,350 fish from 29 species. Alewife were 90% of the total fish catch while Deepwater Sculpin, Round Goby, and Rainbow Smelt comprised the majority of the remaining total catch (3.8, 3.1, and 1.1% respectively). The adult Alewife abundance index for US waters increased in 2017 relative to 2016, however the index for Canadian waters declined. Adult Alewife condition, assessed by the predicted weight of a 165 mm fish (6.5 inches), declined in 2017 from record high values observed in spring 2016. Spring 2017 Alewife condition was slightly less than the 10-year average, but the fall value was well below the 10-year average, likely due to increased Age-1 Alewife abundance. The Age-1 Alewife abundance index was the highest observed in 40 years, and 8-times higher than the previous year. The Age-1 index estimates Alewife reproductive success the preceding year. The warm summer and winter of 2016 likely contributed to the large year class. In contrast the relatively cool 2017 spring and cold winter may result in a lower than average 2017 year class. Abundance indices for Rainbow Smelt, Cisco, and Emerald Shiner either declined or remained at low levels in 2017. Pelagic prey fish diversity continues to be low since a single species, Alewife, dominates the catch. Deepwater Sculpin were the most abundant benthic prey fish in 2017 because Round Goby abundance declined sharply from 2016. Slimy Sculpin density continued to decline and the 2017 biomass index for US waters was the lowest ever observed. Prior to Round Goby proliferation, juvenile Slimy Sculpin comprised ~10% of the Slimy Sculpin catch, but since 2004, the percent of juveniles within the total catch is less than 0.5%, suggesting Round Goby are limiting Slimy Sculpin reproduction. Despite Slimy Sculpin declines, benthic prey fish community diversity has increased as Deepwater Sculpin and Round Goby comprise more of the community.

Lake Ontario↗
USGS2017

Vertical distribution of alewife in the Lake Ontario offshore: Implications for resource use

Oligotrophication of Lake Ontario has led to increased water clarity and an increased proportion of zooplankton residing in the metalimnion during the day, which may affect the utilization of different depth regions for planktivorous fish. We investigated day and night distributions of fish using hydroacoustics and suspended vertical gillnets during the summer of 2013 when a deep chlorophyll layer (DCL) was established. We related fish distributions to concurrent measures of temperature and prey (zooplankton) density. Alewife dominated in vertical gill net catches, indicating that most acoustic targets were alewife. Alewife schooled during the day in the bottom of the mixed layer, and at dusk alewife schools broke up and fish moved towards the surface. We hypothesize this movement followed migrating zooplankton to allow feeding at night; alewife sampled from vertical gillnets fed on cyclopoid copepods and cladocerans, prey groups that migrate into the epilimnion at night. Some alewife remained at the bottom of the mixed layer at night and these fish ate deep-water calanoid copepods such as Limnocalanus . Vertical distributions were best predicted by temperature and the interaction between temperature and zooplankton density. We include uplooking acoustics data to complement our downlooking datasets, which provided evidence for potential bias in downlooking acoustic assessments of alewife due to high proportions of alewife found in the surface exclusion zone. Our approach combining several datasets provides a new perspective to understand summer diel distribution of alewife and the factors driving their distribution.

Journal of Great Lakes Research↗