DOI: 10.5061/dryad.c866t1g9m
title: Fish carcass deposition to suppress invasive lake trout through hypoxia causes limited, non-target effects on benthic invertebrates in Yellowstone Lake

description: Invasive species can have negative effects on native biodiversity and
 ecosystem function, and suppression is often required to minimize the
 effects. However, management actions to suppress invasive species may
 cause negative, unintended effects on non-target taxa. Across the USA,
 lake trout (Salvelinus namaycush) are invasive in many freshwater
 ecosystems, reducing native fish abundance and diversity through predation
 and competition. In an integrated pest management approach, lake trout
 embryos in Yellowstone Lake, Wyoming are suppressed by depositing lake
 trout carcasses onto spawning sites; the carcasses reduce dissolved oxygen
 concentrations as they decay, causing embryo mortality. We conducted a
 field experiment during one ice-free season at four sites in Yellowstone
 Lake to investigate the non-target effects of carcass treatment on benthic
 invertebrates, which could have consequences for native fish diets. While
 overall invertebrate density and biomass did not respond to carcass
 treatment, Chironomidae midges and Sphaeriidae fingernail clams decreased
 in abundance. Carcass treatment altered invertebrate community structure
 based on density, but not biomass. Carcass treatment to suppress invasive
 fish embryos has spatially localized, non-target effects on some benthic
 invertebrate taxa. Given the small spatial extent of carcass treatment
 within the lake, we conclude it is unlikely that carcass treatment will
 alter food availability for native fishes.
description: <em>Study
 area</em> Yellowstone
 Lake is located in Yellowstone National Park in northwestern Wyoming at an
 elevation of 2,357 m (Fig. 1). With a surface area of 340
 km<sup>2</sup>, it is the largest high-elevation lake in North
 America and is generally ice-covered from late December to mid-May.
 Yellowstone Lake is a mesotrophic, dimictic lake that thermally stratifies
 in the summer (Kilham et al. 1996). It has complex bathymetry, with a mean
 depth of 43 m, a maximum depth of 148 m, and hydrothermal vents
 distributed throughout the northern and western regions of the lake
 (Kaplinski 1991). Benthic invertebrate assemblages are dominated by two
 amphipod genera, <em>Hyallela </em>and
 <em>Gammarus</em>, which together comprise approximately 55%
 of invertebrate biomass<em> </em>(Wilmot et al.
 2016). Lake trout are a
 large, piscivorous species that is native throughout Canada and parts of
 the northern United States. Lake trout were first discovered in
 Yellowstone Lake in 1994 and reached peak abundance in 2012, with an
 estimated adult population of nearly 1 million individuals (Koel et al.
 2020a). The lake trout suppression program in Yellowstone Lake began in
 1995 and currently removes about 300,000 adult lake trout each year (Koel
 et al. 2020a). More than 4 million were killed between 1995 and 2021 with
 a majority of the carcasses deposited into deep areas (&gt; 70 m) of
 the lake (Koel et al. 2022). This extensive suppression effort has reduced
 adult lake trout abundance by &gt; 80% since 2012, however,
 recruitment of young lake trout remains high (Koel et al. 2020a). The lake
 trout spawn from late September to early October (Heredia et al. 2021) at
 sites characterized primarily by cobble and bedrock substrate; confirmed
 lake trout spawning sites range in size from 0.3–2.0 ha and comprise 0.03%
 of the total area of Yellowstone Lake (Koel et al. 2020b). To curtail lake
 trout recruitment and improve suppression efficiency, the NPS has
 developed a novel method that deposits carcasses directly on spawning
 areas in the littoral zone of the lake to induce decomposition and cause
 mortality in lake trout embryos via oxygen depletion (Thomas et al. 2019;
 Poole et al. 2020). <em>Carcass
 treatment</em> Carcass treatment occurred at two lake
 trout spawning sites, Flat Mountain Hump and Snipe Point, from 12 August
 to 2 October 2019 (Fig. 1). Of the 14 confirmed lake trout spawning sites
 on Yellowstone Lake (Koel et al. 2020b), these two sites were selected
 because were deep enough and far enough from shore to avoid attracting
 terrestrial wildlife (Thomas et al. 2019) and were adjacent to frequently
 targeted suppression netting locations to facilitate the transportation of
 lake trout carcasses. Carcass treatment only occurred at two spawning
 sites due to limited availability of lake trout carcasses during the
 autumn and logistical difficulties of transporting carcasses across a
 large lake. Two control sites, Flat Mountain Elbow and Elk Point, were
 selected based on similar depths, substrate type, and logistical
 considerations, including avoiding sites frequently targeted by
 suppression netting. Substrate at carcass treatment and control sites was
 dominated by bedrock or cobble (&lt; 250 mm), and the sites varied
 from 2.5 to 9.5 m deep. Limited carcass treatment occurred at both
 treatment sites in 2018 as part of a pilot study, but carcass coverage was
 extremely low (&lt; 3% coverage in October 2018). When sampling began
 in June 2019, no carcass material was observed at Snipe Point, and small
 amounts were observed at Flat Mountain Hump (&lt; 1% coverage).
 Carcass treatment sites were marked with buoys anchored to the substrate
 with concrete blocks. Gill netting crews dumped whole and shredded lake
 trout carcass material from boats within 5 m of marker buoys. Carcass
 dumps occurred opportunistically when gill netting crews had been fishing
 near the carcass treatment sites. Approximately 6,000 kg of fish carcass
 material were deposited at each carcass treatment site. To measure DO, scuba divers secured one
 miniDOT logger (Precision Measurement Engineering) to the substrate
 surface at each carcass treatment and control site. The loggers recorded
 DO (mg/L) at 60-minute increments throughout the entire sampling period
 (17 June–1 October 2019). See Supplement A for details on methods and data
 analysis. To monitor
 carcass cover at the carcass treatment sites, we photographed a 1
 m<sup>2</sup> quadrat placed on the substrate surface using a
 GoPro underwater camera. We took five adjacent photographs of the quadrat
 along a 0º heading, starting directly north of the concrete anchor marking
 the site, and we took five additional photographs along a 180º heading,
 directly south of the concrete anchor. We used ImageJ (Rashband 2018) to
 calculate the percent area of each quadrat covered by carcass material and
 averaged across all 10 quadrats to estimate mean carcass cover every two
 weeks during the carcass treatment period, resulting in four measurements
 per site. <em>Invertebrate collection
 </em> At each site,
 triplicate benthic invertebrate samples were collected monthly for three
 months before carcass treatment started (17 June–11 August 2019) and every
 two weeks (4 sampling intervals) after carcass treatment started (12
 August–1 October 2019). To quantitatively sample benthic invertebrates, we
 used a Scuba diver-operated suction sampler constructed from an electric
 bilge pump mounted on a plastic cutting board with a 500-µm mesh
 collection net (Cross et al. 2011). We randomly placed a 0.25
 m<sup>2</sup> quadrat on the substrate surface and used the
 suction sampler to collect invertebrates within the quadrat. While we did
 not use a quantitative method to randomly select quadrat placement
 locations, we placed the quadrat where the substrate was undisturbed by
 divers, and the same diver placed the quadrat for each sample to reduce
 sampling variability. After surfacing, we rinsed all contents of the
 collection nets into a 500-µm sieve and preserved all material retained by
 the sieve in 75% ethanol. In the laboratory, we subsampled
 invertebrate samples to the smallest fraction that included ≥100
 individuals using a plankton splitter. Subsample fractions ranged from ½
 to 1/16. We sorted invertebrates from debris and organic material and
 identified individuals to the lowest practical taxonomic level, which was
 often genus or family and occasionally order (Rabeni and Wang 2001;
 Merritt et al. 2008). We measured 25 randomly selected individuals of each
 taxon and used published length-mass regressions to calculate biomass
 (AFDM) of each taxon (Bottrell et al. 1976; Benke et al. 1999; Méthot et
 al. 2012). <em>Data
 analysis</em> To
 determine if invertebrate density and biomass changed in response to
 carcass treatment, we assessed the interaction between time (a categorical
 variable with 2 levels: before and during treatment) and treatment using
 linear mixed-effects or zero-inflated negative binomial (ZINB) models. Our
 models included treatment, time, and their interaction as fixed effects,
 and sampling date nested within site as random effects to account for
 temporal and spatial autocorrelation. We used linear mixed effects models
 for most metrics, and we natural log-transformed response variables when
 necessary to meet model assumptions. Because we expected the control and
 treatment sites to change over time due to seasonal variation, we used the
 interaction between time and treatment as evidence of a treatment effect.
 We focused on the three most abundant taxa (<em>Gammarus
 </em>sp. and <em>Hyallela </em>sp. amphipods and
 non-Tanypodinae Chironomidae; Table S1), hypoxia-sensitive taxa
 (Ephemeroptera and Trichoptera), and sessile taxa (Sphaeriidae). We chose
 Ephemeroptera and Trichoptera to represent hypoxia-sensitive taxa instead
 of a metric including Ephemeroptera, Trichoptera, and Plecoptera (EPT,
 Karr 1991) because Plecoptera are not present in Yellowstone Lake. Because
 some taxa were present at control sites but not carcass sites, our
 analyses of Ephemeroptera and Trichoptera density and biomass combined
 taxa within these two orders and only included taxa observed at control
 and carcass sites. We used ZINB models for Ephemeroptera and Trichoptera
 density and Sphaeriidae density, because these data were overdispersed and
 had many zeros (Brooks et al. 2017). We used Akaike information criterion
 corrected for small sample sizes (AICc) to select ZINB models over other
 possible models (Table S2). We did not perform statistical analysis on
 hypoxia-sensitive taxa (i.e., Ephemeroptera and Trichoptera) biomass or
 Sphaeriidae biomass because ZINB models are only appropriate for count
 data (such as abundance), and these overdispersed data did not meet model
 assumptions for other types of analytical tools. Statistical significance
 was tested with an alpha value of 0.1 because of variation expected from
 such a large-scale experiment with low replication, to improve our
 detection of invertebrate responses, and to reduce the possibility of Type
 II error. Model assumptions were examined and met. All statistical
 analyses were conducted in R version 3.6.2 (R Core Team 2019) using the
 lme4 package for linear mixed effects models (Bates et al. 2015) and the
 glmmTMB package for zero-inflated negative binomial models (Brooks et al.
 2017).  We used non-metric
 multidimensional scaling (NMDS) based on Bray-Curtis dissimilarities to
 visualize how invertebrate community structure based on untransformed
 density and biomass responded to carcass treatment (Kruskal 1964; Minchin
 1987). To test if invertebrate community structure changed in response to
 carcass treatment, we used a two-way mixed effects permutational
 multivariate analysis of variance (PERMANOVA) including time, treatment,
 and their interaction as fixed effects and site as a random effect
 (Anderson 2014). We used similarity percentages (SIMPER) analysis to
 identify the taxa that contributed most to differences in multivariate
 position by group, which allowed us to interpret changes in community
 structure (Clarke 1993). Community analysis was conducted using the vegan
 package (Oksanen et al. 2019).
description: Microsoft Excel