DOI: 10.5281/zenodo.18064034
title: Temporal dynamics of mesopelagic fishes within a mesoscale eddy: a Lagrangian perspective — Source data

description: These data support the manuscript “Temporal dynamics of mesopelagic fishes within a mesoscale eddy: a Lagrangian perspective,” currently under review at Limnology and Oceanography Letters. The dataset includes the processed source data underlying the analyses and figures presented in the manuscript.

The file Chl_temporal_variability_Fig1.nc contains processed chlorophyll a concentration data to generate Figure 1 of the associated manuscript. Data were collected from in situ Seaglider profiles, with the glider profiling from the surface to approximately 1,000 m every 6 h and measuring chlorophyll fluorescence at 5 m vertical resolution. For each profile, peak chlorophyll concentrations were identified and aggregated into 24-h bins, summarized as medians with interquartile ranges. Vertical distributional changes were characterized using a dispersion index that quantifies population spread relative to the center of mass, also summarized as daily medians.

The file MOCNESS_zooplanktondistribution_Fig2abc.nc contains dry weight of three zooplankton size classes from nighttime MOCNESS tows (1 m2 mouth opening) aboard the RRS James Cook to generate Figure 2a-c. Three nighttime tows (May 7, 18, and 27 2021) sampled 50 m strata in the upper 200 m, 100 m strata from 200–500 m, and 250 m strata from 500–1000 m. Each sample was split at sea; half was fractionated into five size classes, which were merged for analysis into three size classes (0.2–2.0, 2.0–5.0, and >5.0 mm) for dry weight. Subsamples were processed using the ZooSCAN–Zooprocess–Ecotaxa pipeline. 

The file UVP_zooplankton_Fig2d.nc contains nighttime zooplankton density observed by the Underwater Vision Profiler 5 (UVP5) during May 2021 to generate Figure 2d. Images were processed using Zooprocess and Morphocluster and manually validated in Ecotaxa to include only metazoan zooplankton, excluding Rhizaria. Only nighttime profiles (from sunset through sunrise) collected within the eddy core (15 km from the eddy center) were retained. Data were averaged daily and vertically binned into 20 m depth intervals.

The file Echograms_Fig3ac.nc contains the acoustic data used to generate Figure 3a, c. Data were collected aboard RRS James Cook using a Simrad EK60 echosounder operating continuously at 18 kHz with a 2 s ping interval, 1024 µs pulse duration, and 20 cm vertical resolution. The echosounder was calibrated using the standard sphere method. Data were processed in Echoview v13.1. Samples shallower than 15 m were excluded to minimize near-field effects and surface bubble interference. Data were averaged over 30 pings × 5 depth bins (~70 s × 1 m) and smoothed using a 3-point running median filter in both time and depth to reduce stochastic variability while preserving feature continuity.

The file Echograms_Fig3bd.nc contains the acoustic data used to generate Figure 3b,d. Data were collected aboard RRS James Cook using a Simrad EK60 echosounder operating continuously at 18 and 70 kHz with a 2 s ping interval, 1024 µs pulse duration, and 20 cm vertical resolution. The echosounder was calibrated using the standard sphere method. Data were processed in Echoview v13.1. Samples shallower than 15 m were excluded to minimize near-field effects and surface bubble interference. Data were averaged over 30 pings × 5 depth bins (~70 s × 1 m) and smoothed using a 3-point running median filter in both time and depth to reduce stochastic variability while preserving feature continuity. Analyses focused on surface scattering layers, typically located within the upper 200 m at night and composed of both migratory and non-migratory components. Surface scattering layers were isolated using the frequency-difference method by retaining regions where −3.5 dB re 1 m⁻¹ < ΔSv (18–70 kHz) ≤ 5.3 dB re 1 m⁻¹. Only data with volume backscattering strength (Sv) stronger than −85 dB re 1 m⁻¹ at both frequencies were included.

The file DispersionIndex_NASC_Fig4.nc contains derived acoustic metrics describing the temporal variability of the dispersion index and the Nautical Area Scattering Coefficient (NASC; m² nmi⁻²), used to generate Figure 4. The dispersion index quantifies population spread relative to the center of mass. NASC is a linear measure of integrated acoustic backscatter. Acoustic data from multiple days were aggregated into 15-min time-of-day intervals, excluding intervals with fewer than 50 samples. Two analysis periods were defined to contrast conditions before and after a strong storm event (May 3–19 and May 21–29, 2021), during which scattering layer structure changed markedly.

The file MOCNESS_zooplanktonbiomass_FigS1.nc contains the processed MOCNESS zooplankton biomass data to generate Figure S1. Three paired day–night tows (May 6–7, 17–18, and 26–27, 2021) sampled 50 m strata in the upper 200 m, 100 m strata from 200–500 m, and 250 m strata from 500–1000 m. Each sample was split at sea; half was fractionated into five size classes, which were merged for analysis into three size classes (0.2–2.0, 2.0–5.0, and >5.0 mm) for dry weight. Subsamples were processed using the ZooSCAN–Zooprocess–Ecotaxa pipeline. Tow trajectories intersected different positions relative to the eddy center: 8.1–12.9 km (May 6–7), 17.0–21.6 km (May 17–18), and 18.4–22.0 km (May 26–27). Day–night differences were assessed by comparing integrated biomass in the upper 200 m across size classes.

The file MOCNESS_fish.xlsx contains species composition and size information of mesopelagic fishes from the MOCNESS tows (10 m2 mouth opening) aboard R/V Sarmiento de Gamboa used to support descriptions of mesopelagic fish assemblages in the manuscript. The dataset includes fish taxa/species, counts, and size information for the net that targeted the surface scattering layers (0-100 m).