Temporal dynamics of mesopelagic fishes within a mesoscale eddy: a Lagrangian perspective — Source data

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).本数据集支撑投稿于《湖沼学与海洋学通讯》（Limnology and Oceanography Letters）、目前处于审稿阶段的论文《中尺度涡内中层鱼类（mesopelagic fishes）的时间动态：拉格朗日视角（Lagrangian perspective）》。数据集包含论文中分析与配图所依托的已处理源数据。 文件Chl_temporal_variability_Fig1.nc 包含用于生成对应论文图1的已处理叶绿素a（chlorophyll a）浓度数据。数据采自原位水下滑翔机（Seaglider）剖面观测：滑翔机每6小时从海面至约1000米深度完成一次剖面测量，以5米的垂直分辨率采集叶绿素荧光（chlorophyll fluorescence）数据。针对每一条剖面，识别其中的叶绿素浓度峰值，并将数据汇总至24小时时间箱内，以中位数及四分位距（interquartile ranges）进行统计总结。利用离散指数（dispersion index）表征垂向分布变化，该指数可量化种群相对于质心（center of mass）的扩散程度，结果同样以每日中位数汇总。 文件MOCNESS_zooplanktondistribution_Fig2abc.nc 包含用于生成图2a-c的夜间MOCNESS拖网（MOCNESS tow）采样所得的3个浮游动物粒径类别的干重（dry weight）数据。采样作业搭载英国皇家研究船詹姆斯·库克号（RRS James Cook）开展，拖网网口面积为1平方米。分别于2021年5月7日、18日、27日开展3次夜间拖网，对上200米水深以50米分层采样、200-500米水深以100米分层采样、500-1000米水深以250米分层采样。每份样品在海上进行分装：一半样品被分为5个粒径类别，分析时合并为3个粒径类别（0.2–2.0 mm、2.0–5.0 mm及>5.0 mm）以计算干重。子样品通过ZooSCAN–Zooprocess–Ecotaxa流程完成处理。 文件UVP_zooplankton_Fig2d.nc 包含2021年5月期间采用水下视觉剖面仪5型（Underwater Vision Profiler 5, UVP5）观测得到的夜间浮游动物密度数据，用于生成图2d。图像通过Zooprocess与Morphocluster进行处理，并在Ecotaxa中完成人工校验，仅保留后生浮游动物（metazoan zooplankton）数据，排除有孔虫类（Rhizaria）。仅保留涡旋核心区域（距涡旋中心15公里范围内）的夜间剖面数据（日落至日出时段）。数据按日平均，并以20米为间隔进行垂向分箱处理。 文件Echograms_Fig3ac.nc 包含用于生成图3a、c的声学数据。数据搭载英国皇家研究船詹姆斯·库克号采集，采用西姆拉德EK60（Simrad EK60）回声测深仪，以18 kHz频率连续工作，脉冲间隔（ping interval）为2秒，脉冲时长（pulse duration）1024微秒，垂直分辨率（vertical resolution）20厘米。回声测深仪采用标准球体法（standard sphere method）完成校准。数据在Echoview v13.1软件中进行处理，剔除15米以浅的采样数据以降低近场效应（near-field effects）与表面气泡干扰（surface bubble interference）。数据以30个脉冲×5个深度分箱（约70秒×1米）的规格进行平均，并在时间与深度维度上采用3点滑动中位数滤波（running median filter）进行平滑，以在保留特征连续性的同时降低随机变异（stochastic variability）。 文件Echograms_Fig3bd.nc 包含用于生成图3b、d的声学数据。数据搭载英国皇家研究船詹姆斯·库克号采集，采用西姆拉德EK60回声测深仪，以18 kHz与70 kHz频率连续工作，脉冲间隔为2秒，脉冲时长1024微秒，垂直分辨率20厘米。回声测深仪采用标准球体法完成校准。数据在Echoview v13.1软件中进行处理，剔除15米以浅的采样数据以降低近场效应与表面气泡干扰。数据以30个脉冲×5个深度分箱（约70秒×1米）的规格进行平均，并在时间与深度维度上采用3点滑动中位数滤波进行平滑，以在保留特征连续性的同时降低随机变异。分析聚焦于表层散射层（surface scattering layers）：该层通常夜间分布于上200米水深，包含洄游与非洄游两类组分。通过频差法（frequency-difference method）分离表层散射层，保留满足−3.5 dB re 1 m⁻¹ < ΔSv (18–70 kHz) ≤ 5.3 dB re 1 m⁻¹的区域。仅保留两个频率下体积后向散射强度（volume backscattering strength, Sv）均强于−85 dB re 1 m⁻¹的数据。 文件DispersionIndex_NASC_Fig4.nc 包含用于生成图4的衍生声学指标数据，用于表征离散指数与海面声学散射系数（Nautical Area Scattering Coefficient, NASC；单位：m² nmi⁻²）的时间动态。离散指数用于量化种群相对于质心的扩散程度，NASC为积分声学后向散射的线性度量指标。将多日声学数据汇总至15分钟的日时段区间内，剔除样本量少于50的区间。设置两个分析时段以对比强风暴事件前后的环境条件：2021年5月3日至19日，以及5月21日至29日，该风暴事件期间散射层结构发生显著变化。 文件MOCNESS_zooplanktonbiomass_FigS1.nc 包含用于生成补充图S1（Figure S1）的已处理MOCNESS浮游动物生物量数据。分别于2021年5月6–7日、17–18日、26–27日开展3组成对的昼夜拖网，对上200米水深以50米分层采样、200-500米水深以100米分层采样、500-1000米水深以250米分层采样。每份样品在海上进行分装：一半样品被分为5个粒径类别，分析时合并为3个粒径类别（0.2–2.0 mm、2.0–5.0 mm及>5.0 mm）以计算干重。子样品通过ZooSCAN–Zooprocess–Ecotaxa流程完成处理。拖网轨迹与涡旋中心的相对位置分别为：8.1–12.9 km（5月6–7日）、17.0–21.6 km（5月17–18日）及18.4–22.0 km（5月26–27日）。通过对比各粒径类别在上200米水深的积分生物量，评估昼夜差异。 文件MOCNESS_fish.xlsx 包含搭载于R/V Sarmiento de Gamboa号研究船的MOCNESS拖网（网口面积10平方米）所采集的中层鱼类物种组成与体长信息，用于支撑论文中关于中层鱼类群落（mesopelagic fish assemblages）的描述。数据集包含针对表层散射层（0–100 m）的网采样品的鱼类类群/物种、个体数量与体长信息。