DOI: 10.7291/d1s38t
title: Using light traps to assess larval fish and octopus paralarvae diversity and ontogenetic structure around Santa Catalina Island, CA

description: Monitoring planktonic larvae is important for understanding changes in
 recruitment, range shifts, and reproductive behavior. Here, we used light
 traps to examine the abundance, community diversity, and ontogenetic
 structure of ichthyoplankton and octopus paralarvae at three sites around
 Santa Catalina Island, California, USA across two seasons between 2018 and
 2019. We identified 15,919 fish larvae and 205 octopus paralarvae using
 morphology supplemented by DNA barcoding. We found no differences in
 larval fish diversity or abundance between years or seasons. All octopus
 paralarvae were captured in the summer and were identified as Octopus
 bimaculatus. Cryptic substrate-associated fishes dominated samples,
 especially those from suborder Blennioidei and family Gobiidae. We
 conclude that light traps can be a valuable tool and useful supplement to
 other zooplankton sampling methods, especially in providing a more
 complete assessment of nearshore plankton communities and taxa which have
 been poorly represented in traditional, offshore monitoring programs. They
 may be particularly useful for studying cryptic and substrate-associated
 species whose larvae are often poorly described in the existing
 identification literature.
description: Sampling was conducted from July
 7-25, 2018, March 6-10, 2019, and June 6-July 21, 2019. Samples were
 collected at three coves around Catalina Island, USA: Big Fisherman’s Cove
 (33.4425, -118.5033), Catalina “Cat” Harbor (33.4345, -118.5033), and Two
 Harbors (33.4425, -118.4975). At each site, we sampled zooplankton using
 custom-built cylindrical light traps modeled after Sponaugle &
 Cowen (1996). Traps were made from 505 μm mesh and measured 30 x 60 cm. To
 attract zooplankton, we hung a high-intensity 4 LED white dive light (Tektite Mark III)
 inside the trap. Traps were deployed in the evenings between 17:00 and
 20:00 and collected the following morning after a soak time of 12-14
 hours. Traps were deployed 1-4 m below the surface. To remove any
 potential effect of the traps themselves, we rotated which trap was used
 at each site every night. Within 1 hour of retrieval, traps were washed
 down with fresh water,
 transferring zooplankton into an attached 1L cod end. Zooplankton were
 then immediately preserved in 90% EtOH. Two weeks after initial sample
 collection, alcohol was changed to ensure effective sample preservation.
 Sample volumes were taken
 using the volume displacement method. We removed and counted
 all ichthyoplankton and octopus paralarvae from each sample using a
 dissecting microscope. Fragmented fish tails and fish heads were counted
 as separate individuals; all paralarvae were found intact and were counted
 individually. We used genetic barcoding to further
 confirm species identifications. We selected 87 individuals for barcoding
 that represented commonly identified species, frequent morphotypes that
 did not align with any species in our identification guides, tentative
 identifications from taxa with known identification challenges (e.g.,
 Scorpaenidae), or rare/improbable species. We extracted DNA from these
 individuals using Qiagen DNeasy Blood & Tissue kits (Qiagen, Inc.)
 following standard protocols for subsampled tissue. In most cases, due to
 small size the entire specimen was used for extraction due to the small
 size of the larva. We then amplified a 658 bp region of the COI
 mitochondrial genome using universal primers provided by Carolina
 Biological Supply (VF2_t1/ FishF2_t1/ FishR2_t1/ FR1d_t1). PCR reactions
 had a total volume of 25 μL, composed of 12.5 μL NEB Taq 2× Master Mix,
 10.5 μL primer/loading dye mix, and 2 μL of template DNA. PCR thermal
 cycling consisted of an initial denaturation of 2 min at 94°C followed by
 35 cycles of: 30s at 94°C, 30s at 54°C, and 60s at 72°C. The final
 extension occurred for 10 min at 72°C. Samples were cleaned and sequenced
 using the forward bacterial primer M13F at the UC Berkeley DNA Sequencing
 Facility (https://ucberkeleydnasequencing.com/). The resulting sequence files were examined for quality (Phred scores &gt; 20 were retained) and trimmed by 50-75 bp at both ends. We compared our light trap data with four other surveys of larval fish in the southern California Current: A subset of data from the California Cooperative Oceanic Fisheries Investigation (CalCOFI); a long-term recruitment monitoring program through the Partnership for Interdisciplinary Studies of Coastal Oceans (PISCO); and three shorter-term studies that monitored nearshore larval fish communities using net tows in southern California and southern Baja, MX (Barnett et al. 1984, Stephens et al. 1984, Avendaño-Ibarra et al. 2004).
description: # Using light traps to assess larval fish and octopus paralarvae diversity
 and ontogenetic structure around Santa Catalina Island, CA
 [https://doi.org/10.7291/D1S38T](https://doi.org/10.7291/D1S38T) ##
 Description of the data and file structure Ichthyoplankton records from
 three sites around Santa Catalina Island, CA ### Files and variables ####
 File: Dale_Catalina_Ichthyoplankton_Dryad.csv **Description:** Larval fish
 identifications with sample, taxon, and flexion stage information, along
 with details about sample (date, location). NA values in species and genus
 columns indicate individuals for which species- or genus-level
 identifications were not possible. ##### Variables * sample: Unique ID for
 each plankton sample, comprised of site code and a value. CH = Cat Harbor,
 TH = Two Harbors, BFC = Big Fisherman's Cove * site_name: Name of
 sampling site around Catalina (Big Fisherman's Cove, Cat Harbor or
 Two Harbors) * grouping: General taxonomic grouping according to the most
 prevalent categories of fishes. One of Atherinopsidae, Blenniodei,
 Chaenopsidae, Engraulidae, Gobiidae, Labrisomidae, Pomacentridae, or Other
 Fishes * family: Scientific family name * genus: Scientific genus name *
 species: Scientific species name * scientific_name: Final identification
 to the lowest taxonomic order possible * date_deployed: YYYY-MM-DD * n_s:
 North or south geographic orientation * year: YYYY * month: MM * season:
 General sampling season, one of either "Summer" (June/July) or
 "Spring" (March) * doy: Day of the year, where 1 = January 1st *
 ageclass: General age categories for larval fish. Categories: Pre-flexion
 (termination of the yolk-sac stage until initial notochord flexion),
 Post-flexion (notochord at a 45 angle from notochord axis; posterior
 margin of the upper hypural plate is vertical), Flexion (remaining
 developmental points between pre- and post-flexion), or UnknownAge *
 ageclassnum: Numeric value assigned to each age class. Pre-flexion = 1,
 Flexion = 2, Post-flexion = 3 * n: Total raw number of fish for that
 sample/taxon/age class #### File: Dale_Light_Trap_Data_Dryad.csv
 **Description:** Row-ordered data on each unique trapping event, including
 location, timing, overall number and density of fish larvae and paralarvae
 caught. **Variables:** * sample: Unique ID for each plankton sample,
 comprised of site code and a value. CH = Cat Harbor, TH = Two Harbors, BFC
 = Big Fisherman's Cove * date_deployed: Date deployed in MM/DD/YYYY
 format * site_name: Name of sampling site around Catalina (Big
 Fisherman's Cove, Cat Harbor or Two Harbors) * site: Two-letter site
 code (CH = Cat Harbor, TH = Two Harbors, BFC = Big Fisherman's Cove)
 * n_s: North or south geographic orientation * mpa: Marine protected area
 status * year: YYYY * month: MM * day: DD * season: General sampling
 season, one of either "Summer" (June/July) or "Spring"
 (March) * time_deployed: Time deployed in Pacific Daylight Time (UTC-7). *
 time_retrieved: Time retrieved in Pacific Daylight Time (UTC-7). *
 soak_time: Soak time in HH:MM * soak_hours: Soak time hours component *
 soak_min: Soak time minutes component * soak_min_fraction: Soak time
 minutes as a fraction of 60 minutes (i.e, soak_min = 30 would be
 equivalent to soak_min_fraction = 0.5) * soak_time_standardized: Soak time
 sum of soak_hours + soak_min_fraction * zoop_volume_mL: Volume of
 zooplankton sample (calculated using volumetric displacement method) in mL
 * n_fish: Number of total fish larvae removed from sample * n_ceph: Number
 of total cephalopod paralarvae removed from sample * fish_n_hour: Ratio of
 number of total fish larvae per light trap hour, calculated as
 n_fish/soak_time_standardized * ceph_n_hour: Ratio of number of total
 cephalopod paralarvae per light trap hour, calculated as
 n_ceph/soak_time_standardized #### File:
 Dale_Catalina_Paralarvae_Dryad.csv **Description:** Octopus paralarvae
 data is row-ordered with one row for each individual, with measurement and
 age information, along with details about the sample (date, site). Missing
 measurements are indicated by NA values and indicate individuals for which
 accurate measurements were not able to be taken. ##### Variables *
 individual_id: Paralarvae ID, comprised of two-letter site code, sample
 number, and paralarvae number within that sample * site: Two-letter site
 code (CH = Cat Harbor, TH = Two Harbors, BFC = Big Fisherman's Cove)
 * sample: Unique ID for each plankton sample, comprised of site code and a
 value. CH = Cat Harbor, TH = Two Harbors, BFC = Big Fisherman's Cove.
 * mantle_length_mm: Dorsal mantle length was measured in mm from between
 the middle of the eyes in the dorsal head to the posterior end of the
 mantle * interocular_dist_mm: Interocular distance was measured in mm as a
 straight line between the center of each eye * arm_length1_mm: First arm
 length, measured in mm as the distance from the arm crown to the tip of
 the arm * arm_length2_mm: First arm length, measured in mm as the distance
 from the arm crown to the tip of the arm * avg_arm_length_mm: Average
 between two measured arm lengths * arm_mantle_ratio: The ratio of arm
 length divided by mantle length (A:M ratio) was used as a relative age for
 each individual; individuals with lower A:M values (i.e., shorter arms
 relative to their bodies) were regarded as younger #### File:
 trimmed_sequences.fasta **Description:** FASTA files are listed by vial
 number (refer to barcoding manifest). #### File:
 Dale_Catalina_Barcoding_Manifest_Dryad.xlsx **Description:** Barcoding
 manifest is row-ordered by vial number. Only vials that had high-quality
 readable sequences are retained. NA values in image columns indicate
 orientations that were not photographed. ##### Variables * Vial_no:
 Corresponds to ID in FASTA file * Closest_BLAST_match: Best match
 according to NCBI BLAST tool * Final_identification: Final species/genus
 identification ased on BLAST results and morphology * Perc_identical:
 Percentage identical to closest BLAST match * Dorsal_view: Dorsal
 photograph of specimen, if available * Ventral_view: Ventral photograph of
 specimen, if available * Lateral_view: Lateral photograph of specimen, if
 available #### File: Dale_Catalina_OtherSurveys_Dryad.csv
 **Description:** We compared our data from five other surveys. CalCOFI:
 Extracted standardized larval catch data (larvae/10 m2) for four stations
 off line 90, the closest transect to Catalina. These were stations 35 and
 37 and stations 27.7 and 28. We used data from paired bongo nets and manta
 nets from 2000-2020. Data is available through ERDDAP
 ([https://coastwatch.pfeg.noaa.gov/erddap/index.html](https://coastwatch.pfeg.noaa.gov/erddap/index.html)). PISCO uses Standardized Monitoring Units for the Recruitment of Fishes (SMURFs) to monitor fish recruitment patterns. Like light traps, SMURFs are passive sampling tools suspended 2-3 m below the surface. Each SMURF consists of a cylindrical trap containing plastic barrier and marine snow fencing that imitates preferred recruitment habitat for some species of temperate reef fishes. We compared data from SMURFs placed around the northern California Channel Islands (latitude &lt; 34.1) from 2000-2018. Data is available through DataONE ([https://search.dataone](https://search.dataone).org/view/doi%3A10.6085%2FAA%2FPISCO_UCSB_Fish_Recruitment.1.3).  Finally, we extracted data from three shorter-term studies that monitored nearshore larval fish communities using net tows off the southern California mainland (Palos Verdes and San Onofre) and Bahía Magdalena lagoon in Baja California Sur, Mexico (Barnett et al. 1984, Stephens et al. 1984, Avendaño-Ibarra et al. 2004). Stephens et al. (1984) used diver-towed nets with 505 μm mesh, with collections made just above the substrate (approximately 13m) and at the top of the kelp canopy. Avendano-Ibarra et al. (2004) conducted surface tows using a conical net with 0.6 m mouth diameter and 333 μm mesh. Barnett (1984) sampled from 0-7km offshore and used three different nets (a manta, bongo, and a rolling benthic net), all with 333 μm mesh; this survey primarily caught flexion and post-flexion larvae. The other two net studies did not report the ontogenetic stages of fish captured, though Stephens et al. (1984) would have captured smaller fish with a 505 μm mesh. For all surveys, we calculated the percentage of the total catch contributed by each family at each unique sampling location. NA values indicate catch types not used or relevant to a given survey. ##### Variables * family: Taxonomic family * survey: general survey name * gear: gear type used by survey (nets, recruitment devices, etc). * reported_mesh_um: Reported mesh size in micrometers. * n_larvae: Total number of larvae for that species recorded by the survey * freq_family: Frequency of that family across all fish captured within an individual survey ## Code/software #### **Statistical analyses:** * **R 4.4.1 packages:** Vegan (diversity analyses, PERMANOVA); indicspecies (indicator species analysis) #### Barcoding analysis: * **Software Options**: NCBI's BLAST for handling fasta file ## Access information Publicly accessible locations of the data: * CalCOFI data: [https://coastwatch.pfeg.noaa.gov/erddap/tabledap/erdCalCOFIlrvcnt.html](https://coastwatch.pfeg.noaa.gov/erddap/tabledap/erdCalCOFIlrvcnt.html)  * PISCO SMURF data: [https://search.dataone.org/view/doi%3A10.6085%2FAA%2FPISCO_UCSB_Fish_Recruitment.1.3](https://search.dataone.org/view/doi%3A10.6085%2FAA%2FPISCO_UCSB_Fish_Recruitment.1.3) * Avendaño-Ibarra R, Funes-Rodríguez R, Hinojosa-Medina A, González-Armas R, Aceves-Medina G. 2004. Seasonal abundance of fish larvae in a subtropical lagoon in the west coast of the Baja California Peninsula. Estuarine, Coastal and Shelf Science 61: 125–135. * Barnett AM, Jahn AE, Sertio PD, Watson W. 1984. Distribution of ichthyoplankton off San Onofre, California, and methods for sampling very shallow coastal waters. Fishery Bulletin 82: 97–111. * Stephens J, Pondella D. 2002. Larval productivity of a mature artificial reef: The ichthyoplankton of King Harbor, California, 1974-1997.