DOI: 10.5061/dryad.34tmpg4wc
title: Data from: Associations of commercial fisheries and cold-water corals and sponges

description: The growing threats to deep-sea ecosystems (e.g., offshore wind, seabed
 mining, aquaculture) have the potential to damage these understudied
 systems and to impact the fisheries that they support. However, to date,
 there has not been a uniform assessment identifying which commercially
 landed species are associated with the cold-water corals and other
 structure-forming invertebrates (SFI) found in the deep-sea. We conducted
 a meta-analysis to identify the species of fish and invertebrates landed
 by commercial fisheries in California, USA (2011-2024), and evaluate their
 potential associations with SFI. Captured species are assigned to Landing
 Categories, which range in specificity from individual species to broad
 taxonomic groups. We developed a referenced list of observations
 documenting associations, and use three metrics to identify which of the
 313 Landing Categories are (or are not) associated with SFI: (1) Adjacent:
 species observed within one body length of SFI (target fish) or touching
 SFI (target invertebrates); (2) General Proximity: species observed within
 the general area of SFI or based on modeling; (3) Habitat: species’ depth
 ranges and habitat requirements suggest associations. Approximately 30% of
 Landing Categories were associated with cold-water SFI, but the specific
 percentage varied across metrics (Adjacent: 23%; General Proximity: 27%;
 Habitat: 36%). Commercially targeted fish were more likely to be
 associated with SFI than invertebrates, but many invertebrates had
 undocumented life histories and/or non-specific Landing Categories. This
 study provides a step toward understanding the importance of SFI for
 commercial fisheries and demonstrates the broad co-occurrence between
 commercially landed marine species and living deep-water habitats.
description: <strong>Study Site</strong>
 California’s ocean is characterized by two Marine Ecoregions: a
 temperate, upwelling driven system north of Point Conception (i.e.,
 Montereyan Pacific Transition) and a subtropical, current driven system
 south of Point Conception (i.e., Southern Californian Pacific) (Wilkinson
 et al., 2009). A transitional zone is located at the Point Conception
 geographic break which centers around the northern Channel Islands and
 Santa Barbara Channel. However, the range of the warm-water species can
 extend northward, facilitated by warming effects of El Niños, marine heat
 waves, and the Pacific Decadal Oscillation (Micheli et al., 2020). Due to
 the confluence of these distinct marine regions, California’s marine
 environment is characterized by high biodiversity relative to other
 Western states. The deep sea in California encompasses most state and
 Federal waters, including seamounts, submarine canyons, and relatively
 featureless plains of soft sediment. Such deep-sea areas are targeted by
 commercial and recreational fisheries. In rocky areas, cold-water SFI
 cover cobble, boulders, and bedrock. These deep-sea corals and sponges
 provide habitat for fishes and invertebrates, including those of
 commercial importance. Commercial fishing in California
 takes place in 14,937 km<sup>2</sup> of the ocean (Figure 1).
 Operations include small-scale boats with a single individual or a few
 crew members to large-scale boats with large crews. California’s
 commercial fisheries use a variety of fishing gears and fishing methods,
 ranging from traps, to purse seines, to bottom trawls (CDFW, 2021).
 Fishing operations catch many species of fish and invertebrates that live
 on or near the seafloor, and provide significant revenue to the state
 (CDFW, 2024a). Some areas of the deep ocean are protected as part of
 Federal National Marine Sanctuaries (which allow fishing in most areas),
 California's network of marine protected areas (MPAs), including some
 MPAs that are closed to commercial and recreational fishing such as State
 Marine Reserves (SMR), and Groundfish Exclusion Areas (which are intended
 to mitigate potential impacts to sensitive deep water coral habitat and
 prohibit all commercial and recreational groundfish fishing activity)
 (Figure 1).  <strong>Fisheries
 Dataset</strong> Ex-vessel fisheries landings
 data (Fish Ticket Data) from CDFW document the species of marine life that
 have been caught by commercial fisheries and landed in California. In the
 Fish Ticket dataset, fishers assign landed catches a category name
 (‘Species Name’) and corresponding number (‘Species ID’). In practice, the
 ‘Species Name’ and ‘Species ID’ reporting categories include a
 non-consistent range of species (from single species to whole taxonomic
 groups – see below). To distinguish between species-specific information
 and information about the species that are grouped within a ‘Species Name’
 category, we use the term ‘<em>Landing Categories</em>’ to
 refer to catch data. Many Landing Categories are
 resolved to a single species (e.g., Greenspotted rockfish
 (<em>Sebastes chlorostictus</em>), Market squid
 (<em>Doryteuthis opalescens</em>), Pacific angel shark
 (<em>Squatina californica</em>)). However, other Landing
 Categories are assigned to groups that range in levels of breadth. For
 example, some multi-species categories are based on: (a) broad taxonomic
 groupings (e.g., unidentified molluscs (Phylum Mollusca)); (b) taxonomy
 and habitat preferences (e.g., slope rockfish
 (<em>Sebastes</em> spp.) as defined by CDFW (CDFW, 2021,
 2024b); and (c) groups of species that are difficult to differentiate in
 the field (e.g., Canary (<em>Sebastes pinniger</em>) and
 Vermillion (<em>Sebastes miniatus</em>) Rockfish
 Group). The accuracy of reporting for landings has been
 evaluated for a subset of species, and varies among groups and through
 time. For example, some single species categories of rockfish have high
 accuracy and contain over 95% of a single species (e.g., Greenspotted,
 Yellowtail (<em>S. flavidus</em>), and Copper rockfishes
 (<em>S. caurinus</em>)) (Pearson & Almany, 1995).
 Other categories of rockfishes have been recorded with lower accuracy
 (e.g., Blackgill rockfish (S*. melanostomus)*, Cowcod (<em>S.
 levis</em>), and Splitnose rockfish (<em>S.
 diploproa</em>)) (Pearson & Almany, 1995). Furthermore, the
 precision of records has changed through time - some species are currently
 placed in single species categories, but were lumped into broad categories
 historically (e.g., Greenspotted rockfish vs. Rockfish - unspecified).
 CDFW acquires data from its own fisheries management activities and from
 mandatory reporting requirements on the commercial and recreational
 fishery pursuant to the Fish and Game Code and the California Code of
 Regulations. These data are constantly being updated, and data sets are
 constantly modified. CDFW may provide data upon request, but, unless
 otherwise stated, does not endorse any particular analytical methods,
 interpretations, or conclusions based upon the data it provides.
 <strong>Landing Categories</strong>
 Using the CDFW Fish Ticket dataset, we developed a list of
 specific marine species and multi-species groups that are landed across a
 recent 14-year period (2011-2024). We excluded some Landing Categories
 from our analysis: ten freshwater species, three algae, and herring and
 salmon eggs/roe. From the final list of Landing Categories, we reviewed a
 variety of sources to determine if the species contained within each
 Landing Category were likely associated with SFI during any point in their
 life history. <strong>Metrics of Association with
 Structure-Forming Invertebrates</strong> For the
 species contained within each Landing Category, we evaluated three metrics
 of association with SFI using three commonly applied metrics (Figure 2).
 These measures - used in previous studies of commercially targeted species
 within the U.S. West Coast Exclusive Economic Zone (Rooper et al., 2019;
 Salgado et al., 2018; Yoklavich et al., 2013) - vary in how conservatively
 they identify associations or co-occurrences: 1.    
 <strong>Adjacent</strong> (<em>most
 conservative</em>)<strong>:</strong> <br> Observed
 within one body length of SFI (for fish) or observed touching SFI (for
 invertebrates). This measure scales with body size.
 2.     <strong>General Proximity</strong>
 (<em>moderately
 conservative</em>)<strong>:</strong> <br> Observed
 within the general area of SFI (e.g., within 2 m) or found to be
 associated with SFI using mathematical models. 3.    
 <strong>Habitat & Depth</strong> (<em>least
 conservative</em>): Species’ habitat preferences
 and depth ranges suggest likely associations with cold-water
 SFI. For Habitat & Depth Associations, each
 species was scored as: 0 = not associated
 1 = probable association 2 = definite
 association. Habitat & Depth-based associations
 (scores of 1 or 2) required that species: (a) occur at
 depths &gt;50 m, and (b) are associated with rocky
 habitats or rocky ecotones (transitional areas <br> between
 habitats). Several Landing Categories included more
 than one species. For these multi-species Landing Categories, we assessed
 associations for each species within the group. Within a Landing Category
 if all species were associated for a given metric, the entire Landing
 Category was classified as Associated. Within a Landing Category if
 association information conflicted or the category was broad (e.g.,
 <em>Rockfish – unspecified</em>; <em>Shrimp –
 unspecified</em>), we categorized the Landing Category’s association
 as a multispecies group with mixed associations. Our
 objective was to document associations based on our three metrics defined
 above, and not to evaluate the strength of those associations. Due to the
 widely varying levels of information about species within Landing
 Categories, we considered that species were associated if there was at
 least one documented association. If there were conflicts between
 observations (e.g., where a species in one study was found within one body
 length of SFI, but then other studies where they were found more than one
 body length of SFI) we defaulted to scoring these as ‘Associated’. Species
 observed as Adjacent to SFI were automatically considered General
 Proximity associates, since the latter represents a broader definition.
 Habitat & Depth associations were assessed separately. Species
 determined to be unlikely to associate with SFI (e.g., those occurring at
 depths &lt;50 m or with pelagic life histories) were classified as
 ‘Not Associated’. We evaluated associations across both
 juvenile and adult life history phases. Species exhibiting associations
 during either the juvenile or adult phase were classified as associated.
 We did not distinguish associations by life stage in our dataset because
 life stage–specific association data were lacking for many
 species. <strong>Literature
 Review</strong> We compiled information from
 multiple sources to document associations between target species and SFI.
 We conducted a literature search in Web of Science using the terms:
 <em>(deep sea coral</em> OR cold water coral OR deep water
 coral OR structure forming invertebrate) AND (habitat) AND (California OR
 Washington OR Oregon OR Alaska OR West Coast OR British Columbia) AND
 (associat OR co-occur). This search yielded 198 publications. We screened
 abstracts and reviewed relevant papers for evidence of associations
 involving target species. Using citation chaining and snowball methods, we
 identified additional references. Next, we consulted with regional experts
 to identify additional resources including technical memoranda, natural
 history books, and unpublished reports (e.g., NOAA Cruise Reports).
 Because peer-reviewed literature on associations was limited, gray
 literature was an important data source. To fill remaining gaps, we
 conducted targeted Google Scholar searches of the form: [species name] AND
 (deep sea coral OR cold water coral OR deep water coral OR structure
 forming invertebrate). Finally, we incorporated species life history
 information from online databases such as the CDFW Marine Species Portal
 and SeaLifeBase. This analysis focused exclusively on hard-bottom SFI,
 excluding associations with sea pens, which are characteristic of
 soft-sediment habitats. We focused on data sources from the eastern
 Pacific, except for a few cases for species with broad distributions
 (e.g., swordfish). From each reference, we recorded the study location,
 species, depth range, habitat associations, and type of association. When
 common and extreme depth ranges were provided (see, for example, FishBase)
 we included both estimates. Finally, we recorded if the reference used
 Adjacent, General Proximity, or Depth & Habitat measures of
 association, if relevant. Data sources for each species are summarized in
 Table S1, and the complete list of references reviewed appears in Table
 S2. <strong>Associations by Taxon Group, Species
 Group, and Gear</strong> To provide a baseline
 assessment of associations between cold water SFI and target species we
 summarized how the three standardized association metrics influenced
 association estimates for fish and invertebrate Landing Categories.  To
 evaluate if the three metrics differed in their distribution, we used a
 Pearson’s X<sup>2</sup> Test between associated and
 non-associated measures for all Landing Categories, and for Fish and
 Invertebrate Landing Categories. To evaluate differences in the
 distribution of associations between Fish and Invertebrate Landing
 Categories, we used a Pearson’s X<sup>2</sup> Test for all
 measures.  For this analysis and summary reporting, we grouped probable
 and definite habitat-based associations. To evaluate
 how these associations varied by taxon (fish vs invertebrates) and species
 groups, we grouped Landing Categories into species groups (Leonard
 & Watson, 2011) and summarized the number of Landing Categories
 for each association metric and score. To evaluate how these associations
 varied by gear, we summarized gears into gear groups based on Leonard
 & Watson (2011) and summarized the number of Landing Categories
 for each association metric and score.
description: # Data from: Associations of commercial fisheries and cold-water corals
 and sponges Dataset DOI:
 [10.5061/dryad.34tmpg4wc](10.5061/dryad.34tmpg4wc) ## Description of the
 data and file structure Review of published and grey literature to
 determine which species of commercially landed marine life are or are not
 associated with cold water corals and other structure-forming
 invertebrates for California's commercial fisheries (2010-2024). ###
 Files and variables #### File: selgrath_data_species_group3.csv
 **Description:** table assigning commercially landed fisheries species
 (Species ID) from California (2010-2024) to species groups * SpeciesGroup
 = type of species * species_group2= fish, invertebrate, or algae #####
 Variables * SpeciesName: species name * species_id: species ID *
 SpeciesGroup: *type of species* * species_group2: fish, invertebrate, or
 algae #### File: selgrath_dsc_val_associations_freshwater2.csv
 **Description:** Binary table identifying commercially landed fisheries
 species (Species ID) from California (2010-2024) that are (1) or are not
 (0) freshwater species. ##### Variables * species_id: ID for each CDFW
 landing category (LC) * freshwater: binary: freshwater spp (1) or
 non-freshwater spp (0) #### File: selgrath_table_s1_onlylandedspp.csv
 **Description:**  - File contains data and references about habitat
 associations for the lowest taxonomic unit (e.g., Landings Categories,
 species) for California’s commercially landed species of marine life,
 including references. These data describe associations of commercially
 landed marine life with cold water corals and structure-forming
 invertebrates. For each Landing Category, we evaluated three metrics of
 association with SFI (Figure 2). These measures have all been used in past
 studies (Rooper et al., 2019; Salgado et al., 2018; Yoklavich et al.,
 2013), and range in how conservative they are in identifying associations
 and/or co-occurrences: (1)   **Adjacent:** observed within one body length
 of SFI (fish) or observed touching SFI (invertebrates). This measure
 scales with body size. (*most conservative*) (2)   **General Proximity:**
 observed within the general area of SFI (e.g., within 2 m) or found to be
 associated with SFI using mathematical models. (*moderately conservative*)
 (3)   **Habitat:** species’ depth ranges and habitat associations suggest
 that associations with deep-sea SFI are likely to exist. (*least
 conservative*) Scored as:       0 = not associated       1 = probable
 association       2 = definite association Habitat association scores of 1
 and 2 had depth and habitat requirements: (a) found in depths greater than
 50 m; and (b) associated with rocky habitats or rocky ecotones (edges
 between habitats). ##### Variables * species_id: ID for each CDFW landing
 category (LC) * group: species group - fish, invertebrate, algae *
 common_name: species' common name * genus:  * species: * depth_min_m:
 minimum depth in meters (# in parentheses is extreme range rarely
 observed) * depth_max_m: maximum depth in meters (# in parentheses is the
 extreme range rarely observed) * adjacent: adjacent association *
 general_prox: general proximity association * habitat_depth: habitat and
 depth association * habitat: habitat requirements * References: references
 about this species or landing category #### File:
 selgrath_table_s2_data_sources.csv **Description:**    - List of
 references that were consulted to assess if California’s commercially
 landed species of marine life were associated with cold-water corals and
 other structure-forming invertebrates. ##### Variables * Type: type of
 reference * References: specific reference * Country: country reference
 focused on * Region: region reference focused on #### File:
 selgrath_selgrath_table_S3_associations_species_groups.csv
 **Description:**   For California’s commercial fisheries (2010-2024),
 counts of associated Landing Categories by species group and type of
 association for three metrics of association with structure-forming
 invertebrates.  **Variables** * species_group - summarized groups of
 related species and landing categories for commercially landed species. *
 score - type of association for the landing categories summarized within
 the species group. Scores are: \   - Associated; \   - Multispecies groups
 (landing categories where specific species are not specified (e.g.,
 "unidentified mollusks"));\   - No data; \   - Not Associated. *
 adjacent - count of species groups that have this score based on the
 Adjacent metric of associations. * general_proximity - count of species
 groups that have this score based on the General Proximity metric of
 associations. * habitat_depth_definite - count of species groups that have
 this score based on the Depth and Habitat definition of associations. Note
 that the No Data category is not relevant for the Depth and Habitat
 metric. * habitat_depth_probable - count of species groups that have this
 score based on the Adjacent definition of habitat associations. #### File:
 selgrath_selgrath_table_s4_associations_gear.csv **Description:**   For
 California’s commercial fisheries (2010-2024), counts of associated
 Landing Categories by fishing gear group for three metrics of association
 with structure-forming invertebrates.  * gear_id - unique ID for the gear
 type * gear_name - name of the gear type * gear_group - summarized groups
 of similar fishing gears (e.g., hook and line) * adjacent - count of
 commercially landings categories that are captured by this type of fishing
 gear and associated with cold water structure forming invertebrates based
 on the Adjacent association metric  * general_proximity - count of
 commercially landings categories that are captured by this type of fishing
 gear and associated with cold water structure forming invertebrates based
 on the General Proximity association metric  * habitat_depth - count of
 commercially landings categories that are captured by this type of fishing
 gear and associated with cold water structure-forming invertebrates based
 on the Habitat and Depth association metric ## Code/software Data is in
 non-proprietary data formats. Data analysis was conducted in R. R code is
 available at github.com/jselgrath/dsc_fishery_associations and on Zendo
 (10.5281/zenodo.17785322). R code is organized by a driver file
 (driver.R), which has descriptions of each code chunk, and the input and
 output of each code chunk. ## Access information Other publicly accessible
 locations of the data: * see references * Raw fisheries data can be
 requested from the California Department of Fish and Wildlife, but it is
 not publicly available.