Using light traps to assess larval fish and octopus paralarvae diversity and ontogenetic structure around Santa Catalina Island, CA
Data files
Sep 09, 2025 version files 258.58 MB
-
Dale_Catalina_Barcoding_Manifest_Dryad.xlsx
258.29 MB
-
Dale_Catalina_Ichthyoplankton_Dryad.csv
210.05 KB
-
Dale_Catalina_OtherSurveys_Dryad.csv
4.77 KB
-
Dale_Catalina_Paralarvae_Dryad.csv
11.96 KB
-
Dale_Light_Trap_Data_Dryad.csv
7 KB
-
README.md
10.16 KB
-
trimmed_sequences.fasta
43.28 KB
Abstract
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.
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).
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 < 34.1) from 2000-2018. Data is available through 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
- PISCO SMURF data: 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.
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 > 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).