Assessing small pelagic fish trends in space and time using piscivore diet data

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# Does prey drive availability of bluefish?

## Bluefish, *Pomatomus saltatrix*

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![Bluefish illustration, credit NOAA Fisheries](https://media.fisheries.noaa.gov/styles/original/s3/2022-08/640x427-Bluefish-NOAAFisheries.png)
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Bluefish diet in the Northeast US  
<img src="https://media.fisheries.noaa.gov/styles/original/s3/2022-08/640x427-Squid-Longfin-v1-NOAAFisheries.png" width="25%" /><img src="https://objects.liquidweb.services/images/201909/robert_aguilar,_serc_48650727166_3ce8edc47d_b.jpg" width="25%" /><img src="https://media.fisheries.noaa.gov/styles/original/s3/2022-08/640x427-Butterfish-NOAAFisheries.png" width="25%" /><img src="https://media.fisheries.noaa.gov/styles/original/s3/2022-09/640x427-Scup-NOAAFisheries_0.png" width="25%" /><img src="https://media.fisheries.noaa.gov/styles/original/s3/2022-08/640x427-Herring-Atlantic-NOAAFisheries.png" width="25%" /><img src="https://media.fisheries.noaa.gov/styles/original/s3/2022-08/640x427-Mackerel-Atlantic-NOAAFisheries.png" width="25%" /><img src="https://diveary.com/img/species/cache/323__jpg.jpeg" width="25%" /><img src="https://www.vims.edu/research/departments/fisheries/programs/juvenile_surveys/netnotes_listing/_photosets/0910_dec_jan/_northernsandlance.jpg" width="25%" /><img src="https://media.fisheries.noaa.gov/styles/original/s3/2022-09/640x427-Hake-Silver-NOAAFisheries.png" width="25%" /><img src="https://media.fisheries.noaa.gov/styles/original/s3/2021-03/squid_illex_nb_w_0.png" width="25%" /><img src="https://media.fisheries.noaa.gov/styles/original/s3/2021-01/640x427-Atlantic_Menhaden_NB_W.jpg" width="25%" />
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Northeast Fisheries Science Center Diet Data Online: https://fwdp.shinyapps.io/tm2020/
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We built a spatial "forage index" based on 20 prey groups using stomach contents of 22 predators 
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Changing distribution and abundance of small pelagics may drive changes in predator distributions, affecting predator availability to fisheries and surveys. However, small pelagic fish are difficult to survey directly, so we developed a novel method of assessing small pelagic fish aggregate abundance via predator diet data. We used piscivore diet data collected from multiple bottom trawl surveys within a Vector Autoregressive Spatio-Temporal (VAST) model to assess trends of small pelagics on the Northeast US shelf. The goal was to develop a spatial “forage index” to inform survey and/or fishery availability in the bluefish (Pomatomus saltatrix) stock assessment. Using spring and fall surveys from 1973-2020, 20 small pelagic groups were identified as major bluefish prey using the diet data. Then, predators were grouped by diet similarity to identify 19 piscivore species with the most similar diet to bluefish in the region. Diets from all 20 piscivores were combined for the 20 prey groups at each surveyed location, and the total weight of small pelagic prey per predator stomach at each location was input into a Poisson-link delta model to estimate expected prey mass per predator stomach. Best fit models included spatial and spatio-temporal random effects, with predator mean length, number of predator species, and sea surface temperature as catchability covariates. Spring and fall prey indices were split into inshore and offshore areas to reflect changing prey availability over time in areas available to the recreational fishery and the bottom trawl survey, and also to contribute to regional ecosystem reporting

Using NEFSC bottom trawl survey diet data from 1973-2021, 20 small pelagic groups were identified as major bluefish prey with 10 or more observations (in descending order of observations): Longfin squids (*Doryteuthis* formerly *Loligo* sp.), Anchovy family (Engraulidae), bay anchovy (*Anchoa mitchilli*), Atlantic butterfish, (*Peprilus triachanthus*), Cephalopoda, (*Anchoa hepsetus*), red eye round herring (*Etrumeus teres*), Sandlance (*Ammodytes* sp.), scup (*Stenotomus chrysops*), silver hake (*Merluccius bilinearis*), shortfin squids (*Illex* sp.), Atlantic herring (*Clupea harengus*), Herring family (Clupeidae), Bluefish (*Pomatomus saltatrix*), silver anchovy (*Engraulis eurystole*), longfin inshore squid (*Doryteuthis pealeii*), Atlantic mackerel (*Scomber scombrus*), flatfish (Pleuronectiformes), weakfish (*Cynoscion regalis*), and Atlantic menhaden (*Brevoortia tyrannus*).

Prey categories such as fish unidentified, Osteichthyes, and unidentified animal remains were not included in the prey list. Although unidentified fish and Osteichthyes can comprise a significant portion of bluefish stomach contents, we cannot assume that unidentified fish in other predator stomachs represent unidentified fish in bluefish stomachs.

Image credits: Striped and bay anchovy photo--Robert Aguilar, Smithsonian Environmental Research Center; redeye round herring photo--https://diveary.com ; sandlance photo--Virginia Institute of Marine Science; all others NOAA Fisheries.

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## Aggregating predators: diet similarity to bluefish in gold

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<img src="20230201_BluefishRT_ForageIndexSummary_Gaichas_files/figure-html/unnamed-chunk-2-1.png" width="504" />
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<img src="https://media.fisheries.noaa.gov/styles/original/s3/2022-08/640x427-Bluefish-NOAAFisheries.png" width="25%" /><img src="https://media.fisheries.noaa.gov/styles/original/s3/2022-07/640x427-Cod-Atlantic-NOAAFisheries.png?itok=kNKcZ7iV" width="25%" /><img src="https://media.fisheries.noaa.gov/styles/original/s3/2022-08/640x427-Shark-SpinyDogfish-NOAAFisheries.png?itok=cdjTG3Hz" width="25%" /><img src="https://media.fisheries.noaa.gov/styles/original/s3/2022-09/640x427-Monkfish-NOAAFisheries.png?itok=7JAgAz-u" width="25%" /><img src="https://media.fisheries.noaa.gov/styles/original/s3/2022-09/640x427-Flounder-Summer-NOAAFisheries.png?itok=II2ii-Qw" width="25%" /><img src="https://media.fisheries.noaa.gov/styles/original/s3/2022-08/640x427-Pollock-Atlantic-NOAAFisheries.png?itok=ZFoDB-Qr" width="25%" /><img src="https://media.fisheries.noaa.gov/styles/original/s3/2022-09/640x427-Hake-Red-NOAAFisheries.png?itok=SyCYEmmm" width="25%" /><img src="https://media.fisheries.noaa.gov/styles/original/s3/2022-08/640x427-Halibut-Atlantic-right-NOAAFisheries.png?itok=uPvRdIBx" width="25%" /><img src="https://media.fisheries.noaa.gov/styles/original/s3/2022-08/640x427-StripedBass-NOAAFisheries.png?itok=4ZQoQM0S" width="25%" /><img src="https://media.fisheries.noaa.gov/styles/original/s3/2020-12/640x427-Hake_White_NB_W.jpg?itok=yHy_AuTT" width="25%" /><img src="https://media.fisheries.noaa.gov/styles/original/s3/2022-09/640x427-Hake-Silver-NOAAFisheries.png" width="25%" /><img src="https://media.fisheries.noaa.gov/styles/original/s3/dam-migration/640x427-cusk.jpg?itok=u0fw0hiv" width="25%" /><img src="https://media.fisheries.noaa.gov/styles/original/s3/2022-08/640x427-Squid-Longfin-v1-NOAAFisheries.png" width="25%" /><img src="https://media.fisheries.noaa.gov/styles/original/s3/2021-03/squid_illex_nb_w_0.png" width="25%" /><img src="https://github.com/NOAA-EDAB/presentations/raw/master/docs/EDAB_images/weakfishASMFC.png" width="25%" /><img src="https://photolib.noaa.gov/Portals/0//GravityImages/36881/ProportionalFixedWidth/sanc100698384x800x800.jpg" width="25%" />

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All size classes of 50 fish predators captured in the NEFSC bottom trawl survey were grouped by diet similarity to identify the size classes of piscivore species with the most similar diet to bluefish in the region.  Diet similarity analysis was completed using the Schoener similarity index (@schoener_nonsynchronous_1970; B. Smith, pers. comm.), and is available available via [this link on the NEFSC food habits shiny app](https://fwdp.shinyapps.io/tm2020/#4_DIET_OVERLAP_AND_TROPHIC_GUILDS). The working group evaluated several clustering methods to develop the predator list (see [this link with detailed cluster results](https://sgaichas.github.io/bluefishdiet/PreySimilarityUpdate.html)).

Predators with highest diet similarity to Bluefish from the NEFSC diet database (1973-2020) include Atlantic cod, Atlantic halibut, buckler dory, cusk, fourspot flounder, goosefish, longfin squid, shortfin squid, pollock, red hake, sea raven, silver hake, spiny dogfish, spotted hake, striped bass, summer flounder, thorny skate, weakfish, and white hake. The NEAMAP survey operates closer to shore than the current NEFSC survey. The NEAMAP dataset includes predators sampled by the NEFSC survey and adds two species, Spanish mackerel and spotted sea trout, not captured by the NEFSC survey offshore but included based on working group expert judgement of prey similarity to bluefish. Predator size classes included are listed in Table 2 of the forage fish index working paper at [this link](https://sgaichas.github.io/bluefishdiet/VASTcovariates_forageindex_WP.html).

Image credits: Weakfish and Spanish mackerel-- https://marinefishesofgeorgia.org ; spotted seatrout-- https://fishinginmiami.com ; Sea Raven photo 2/11/2019 11:07:56 AM, Photographer: Andrew J. Martinez, Location: Massachusetts, Stellwagen Bank NMS; all others NOAA Fisheries.

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## Spatial partitioning: examining forage trends at multiple scales

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<img src="20230201_BluefishRT_ForageIndexSummary_Gaichas_files/figure-html/maps-1.png" alt="Maps of key areas for Bluefish assessment indices. The full VAST model grid is shown in brown." width="33%" /><img src="20230201_BluefishRT_ForageIndexSummary_Gaichas_files/figure-html/maps-2.png" alt="Maps of key areas for Bluefish assessment indices. The full VAST model grid is shown in brown." width="33%" /><img src="20230201_BluefishRT_ForageIndexSummary_Gaichas_files/figure-html/maps-3.png" alt="Maps of key areas for Bluefish assessment indices. The full VAST model grid is shown in brown." width="33%" />
<p class="caption">Maps of key areas for Bluefish assessment indices. The full VAST model grid is shown in brown.</p>
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Indices for aggregate small pelagics from piscivore stomachs can be calculated for any subset of the full model domain. Bias correction of the resulting indices is then applied <a name=cite-thorson_implementing_2016></a>([Thorson, et al., 2016](https://www.sciencedirect.com/science/article/pii/S0165783615301399)).

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NEFSC survey strata definitions are built into the VAST `northwest-atlantic` extrapolation grid already. We defined additional new strata to address the recreational inshore-offshore 3 mile boundary. The area within and outside 3 miles of shore was defined using the `sf` R package as a 3 nautical mile (approximated as 5.556 km) buffer from a high resolution coastline from the`rnaturalearth` R package. This buffer was then intersected with the current `FishStatsUtils::northwest_atlantic_grid` built into VAST and saved using code [here](https://github.com/sgaichas/bluefishdiet/blob/main/VASTcovariates_updatedPreds_sst_3mi.Rmd#L49-L94). Then, the new State and Federal waters strata were used to split NEFSC survey strata where applicable, and the new full set of strata were used along with a modified function from `FishStatsUtils::Prepare_NWA_Extrapolation_Data_Fn` to build a custom extrapolation grid for VAST as described in detail [here](https://sgaichas.github.io/bluefishdiet/VASTcovariates_finalmodbiascorrect_3misurvstrat.html).

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## Results: Fall Forage Indices by area

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<img src="20230201_BluefishRT_ForageIndexSummary_Gaichas_files/figure-html/WHAMfall-1.png" alt="Time series of VAST estimated fall forage indices for input into the bluefish assessment, 1985-2021" width="504" />
<p class="caption">Time series of VAST estimated fall forage indices for input into the bluefish assessment, 1985-2021</p>
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Northeast US VAST estimated Fall forage biomass density &rarr;
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