Access the associated article at: https://doi.org/10.1093/jcbiol/ruaf017

We have submitted our raw files within multiple files including the CTD data (CTD_Data_18_23.csv), our larval density data (Larval_Density_18_23.csv), zooplankton data (Zooplankton_18_23.csv) and carapace data for both Stage I (Stg1_CarapaceLengths_19_23.csv) and postlarvae/Stage IV (PL_CarapaceLengths_18_23.csv).

Description of the data and file structure

Throughout the files listed below, DOY refers to Day-Of-Year, and within the majority of files there is a date field, though Day, Month, and Year are also provided for quick comparisons. Fields specifically used in analyses are detailed below. The "Site" or "Station" fields are interchangeable, and correspond to the four larval survey sites (2, 3, 8, 9) as described within the manuscript linked to above. SI = Stage 1 larvae, PL = postlarvae / Stage IV

CTD_Data_18_23.csv

All data were collected at Site 9

• Record_no is a running unique number for all records.
• Depth Depth in meters at which the measurement was taken
• Fluorescence fluorescence_mgm3 = fluorescence in mg/m3
• Temp temp_c = Temperature in Celsius
• Salinity salinity_psu = Salinity in psu
• Depth_binned Depth from above, binned to nearest meter

Larval_Density_18_23.csv

• SI_density - USEME: Density of SI as calculated by (raw count / m3 filtered water * 1000 = density 1000m-3)
• SII_density - USEME: Density of SII as calculated by (raw count / m3 filtered water * 1000 = density 1000m-3)
• SIII_density - USEME: Density of SIII as calculated by (raw count / m3 filtered water * 1000 = density 1000m-3)
• PL_density - USEME: Density of SIV as calculated by (raw count / m3 filtered water * 1000 = density 1000m-3)
• SI_abundance -Extra field calculated as abundance (1000-2)
• SII_abundance -Extra field calculated as abundance (1000-2)
• SIII_abundance -Extra field calculated as abundance (1000-2)
• PL_corr_abundance -Extra field calculated with an estimate of PL's spending 0.65 of their time at the surface. See manuscripts by Eric Annis. (Density / 2 / 0.65)
• PL_uncorr_abundance - Extra field of density / 2 See manuscripts by Eric Annis on previous larval work.

Zooplankton_18_23.csv

• Source Origin of the dataset (DMR = Department of Marine Resources)
• Depth_Sampled = Maximum depth of vertical net (100 meters)
• Depth_Strata = Integrated
• TOTAL = Total zooplankton measurement
• Remaining fields = The remaining fields are nested taxonomic hierarchies, so the total above does not equal the sum of all remaining columns. For example, some taxa are identified and counted to specific epithet, while others are only counted at the family level. Columns for the family level of the majority of taxa are provided, which are a sum of all lower taxa counted.

Stg1_CarapaceLengths_19_23.csv

• Stg1_CL Carapace length of stage I larvae in millimeters (mm) as measured from the back of the eye socket parallel down the carapace to the dip in the edge of the carapace.

PL_CarapaceLengths_18_23.csv

• PL_CL Carapace length of stage IV larvae in millimeters (mm) as measured from the back of the eye socket parallel down the carapace to the dip in the edge of the carapace.
• Sample_year Year of sampling
• Sample_year_2 Year of sampling

Notable survey timeline events:

• Survey leads
  2018 – 2022: Jes Waller
  2023 – Present: Heather Glon
• Vessel use
  2018 – 2023: Bureau of Marine Science 26’ Whaler
• Larval Time Series notes
  Typically, our time series aims to sample every other week in June, every week in July & August, and every other week in September. However, due to vessel, weather, and personnel constraints, these sampling dates have varied throughout the survey with interannual variability in both the start date and end date of sampling. Sampling has been conducted most consistently throughout July and August in all years, representing the core sampling period of the time series. The team attempts to go out weekly or biweekly, but due to fog or afternoon winds, may cut their sampling days short or only sample the inner two sites. Variability in seasonal and spatial coverage reflects operational and environmental considerations and does not indicate changes to core sampling protocols.

Sampling began in July during 2018 and 2019, with no collections conducted in June during those years. Beginning in 2020, sampling initiation shifted earlier, with collections starting in June for all years through 2024. The extent of June sampling varied among years, ranging from a single mid-June sampling event to multiple sampling events spanning early, mid, and late June.

Sampling extended into September in all years, though the number of September sampling events varied interannually. Some years include limited early-September sampling, while others extended into late September.

Brief summary of yearly sampling intervals:
• 2018: July–September
• 2019: July–September
* Some sampling dates in July & August of 2019 are missing due to engine failure.
• 2020: Mid-June–September
• 2021: Early June–early September
• 2022: Mid-June–late September
• 2023: Mid-June–late September

Data quality & use considerations

Known Limitations

• Interannual variability in sampling dates and seasonal coverage.
• Changes in environmental sensor availability through time.
• Incomplete calibration history for select CTD sensors.

These limitations should be considered when conducting trend, phenology, or environmental analyses.

Use Constraints

• These data are provided for scientific and management use. Users are responsible for ensuring appropriate interpretation.
• Users should not assume uniform temporal or spatial coverage across years, as sampling start and end dates vary interannually.
• Comparisons among years should be limited to overlapping sampling periods unless differences in seasonal coverage are explicitly addressed.
• Users should not infer changes in sampling protocols from gaps or variability in temporal or spatial coverage.
• Environmental (CTD) data may be provided in a largely raw format and may require user-led QA/QC prior to analysis. Check with the survey lead to establish data condition if unsure.
• Sampling is conducted at a fixed set of established stations that are sampled repeatedly through time and are not randomly selected.
• Analyses should not extrapolate results beyond sampled stations or assume representativeness of unsampled areas without additional justification.
• Fluorescence data are provided for contextual purposes only and should be used cautiously due to incomplete calibration history.
• Any redistribution or publication of derived products should include appropriate citation of the ME DMR larval lobster survey and associated metadata, and notification to the survey lead.
• Users are encouraged to contact ME DMR prior to data use and before publication for clarification of data limitations or interpretation, particularly for cross-year or environmental analyses.

Data Quality and Considerations

Temporal Coverage

• Sampling was conducted seasonally between 2018 and 2024, with consistent coverage during July and August in all years.
• June, September, and October sampling occurred inconsistently among years and may reflect operational constraints rather than biological absence or presence, particularly affecting interpretation of early-stage (Stage I) larval densities.

Fixed-Station Sampling Design

• Larval and environmental data are collected at a consistent set of fixed stations (site IDs) to support time-series analyses.
• Fixed-station sampling is intended to characterize temporal variability at known locations, not to estimate spatial distributions across the broader study area.
• Comparisons among stations should account for site-specific characteristics (e.g., depth, exposure, proximity to shore or convergence zones) that are consistent through time but differ among stations.

Larval Abundance Data

• Larval abundance is reported as counts per effort and should be interpreted in conjunction with deployment duration, flowmeter readings, and calibration constants (see Glon et al. 2025).
• Effort- and catch-level comments may document factors affecting sampling efficiency (e.g., seaweed loading, flowmeter issues).

Environmental (CTD) Data

• CTD data has fluorescence available for some years but lacks recent sensor calibration. Use caution when relying on these data.
• Beginning in 2024, pH and dissolved oxygen sensors were added, and spatial coverage expanded to include most sites.
• Environmental data include both downcast and upcast measurements; users are advised to preferentially use upcast data, except in documented cases (and in 2018) where bottom contact occurred.
• Surface measurements within the top 1 m may be affected by CTD deployment or retrieval from a small vessel; caution is advised when interpreting near-surface values.

Additional Considerations

• The fixed-station, repeated-sampling design supports analyses of within-season and interannual changes in larval timing at known locations.
• Interannual variability in sampling dates must be explicitly accounted for when interpreting onset, peak, or termination of the larval season.
• Users are encouraged to use effort-standardized metrics and to clearly report the temporal window analyzed.
• Apparent shifts in phenological metrics may reflect sampling design and effort rather than true biological change.

Sharing/Access information

Larval survey timeseries

Link to a data dashboard updated annually on the larval survey data is available at: https://www.maine.gov/dmr/science/species-information/maine-lobster/lobster-life-stages-and-dmr-surveys/larval-lobster-surveys

Code/Software

Code for analyses and figures are largely contained within the R script markdown file summarized in: Larval_Manuscript_Clean_Script_FIGURE_SAVE.Rmd