Momma's larvae: Maternal oceanographic experience and larval size influence early survival of rockfishes

Fennie, Hamilton1 ; Ben-Aderet, Noah2 ; Bograd, Steven3 ; Kwan, Garfield4 ; Santora, Jarrod3 ; Schroeder, Isaac5 ; Thompson, Andrew3

Published Oct 30, 2023 on Dryad. https://doi.org/10.7291/D1Q96H

Abstract

Identifying factors that affect larval mortality is critical for understanding the drivers of fish population dynamics. Although larval fish mortality is high, small changes in mortality rates can lead to large changes in recruitment. Recent studies suggest maternal provisioning can dramatically affect the susceptibility of larvae to starvation and predation, the major sources of early-life mortality. We measured otolith core width-at-extrusion and validated that this is a proxy for larval size-at-extrusion for eight species of rockfishes (genus Sebastes) to examine the influence of initial larval size on larval growth and survival and to understand how oceanographic conditions experienced by gestating females affect larval size (i.e., quality). Otolith core width-at-extrusion was significantly positively related to larval rockfish recent growth rate (5/7 species with sufficient sample size) and survival (all eight species). This suggests that individuals that are larger at extrusion generally grow faster and are more likely to survive early life stages. Otolith core width-at-extrusion was positively related to higher presence of Pacific Subarctic Upper Water and was negatively related to warmer, saline waters at the depths gestating mothers inhabited during the months prior to larval collection. In addition, otolith core width was larger further from fishing ports, possibly because these locations were historically less fished, contained more older, larger females, and/or had inherently better habitat quality (higher Pacific Subarctic Upper Water) than sites closer to shore. These results indicate that the environmental conditions female rockfish experience during gestation drive the size of the larvae they produce and impact larval growth and survival.

README

This README file was generated on 2023-10-20 by Will Fennie

GENERAL INFORMATION

Title of Dataset: Momma's larvae: maternal oceanographic experience and larval size influence early survival of rockfishes
Author Information A. Corresponding Author Contact Informatino Name: Will Fennie Insititution: NOAA Alaska Fisheries Science Center Address: Seattle, WA Email: will.fennie@noaa.gov
Date of collection: Fall 1997 - Winter 2013
Geographic location of collection: Southern California Bight, California, USA
Information about funding sources that supported the collection of the data: Future Seas (NOAA Climate and Fisheries Adaptation Program grant number NA20OAR4310507), and CCE LTER (NSF OCE-2224726).

SHARING/ACCESS INFORMATION

Licenses/restrictions placed on the data: CC0 1.0 Universal (CC0 1.0) Public Domain
Links to publications that cite or use the data:

Thompson, A. R., Hyde, J. R., Watson, W., Chen, D. C., & Guo, L. W. (2016). Rockfish assemblage structure and spawning locations in southern California identified through larval sampling. Marine Ecology Progress Series, 547, 177-192.

Thompson, A. R., Chen, D. C., Guo, L. W., Hyde, J. R., & Watson, W. (2017). Larval abundances of rockfishes that were historically targeted by fishing increased over 16 years in association with a large marine protected area. Royal Society open science, 4(9), 170639.

Links to other publicly accessible locations of the data: None
Links/relationships to ancillary data sets: None
Was data derived from another source? No A. If yes, list source(s): NA
Recommended citation for this dataset: Fennie, H. W., Ben‐Aderet, N., Bograd, S. J., Kwan, G. T., Santora, J. A., Schroeder, I. D., & Thompson, A. R. (2023). Data fomr: Momma's larvae: Maternal oceanographic experience and larval size influence early survival of rockfishes. Dryad Digital Repository.https://doi.org/10.7291/D1Q96H.

Data and file overview:

File list:

a) age_size.rda
b) calcofi stations with date and time 98-13.csv
c) Fall_OC_growth_ENV_PSUW.rda
d) winter_OC_age_ENV_PSUW.rda
e) Mean_winter_OC_dist_growth_resid_goodei_ENV_PSUW.rda
f) Mean_winter_OC_dist_growth_resid_hopkinsi_ENV_PSUW.rda
g) Mean_winter_OC_dist_growth_resid_jordani_ENV_PSUW.rda
h) No dataset for S. mystinus (too few fish >=3 days old - analysis could not run with so few data points)
i) Mean_winter_OC_dist_growth_resid_paucispinis_ENV_PSUW.rda
j) Mean_winter_OC_dist_growth_resid_rufus_ENV_PSUW.rda
k) Mean_winter_OC_dist_growth_resid_serranoides_ENV_PSUW.rda
l) Mean_winter_OC_dist_growth_resid_wilsoni_ENV_PSUW.rda
m) rockfish_age.rda

Relationship between files, if important: None
Additional related data collected that was not included in the current data package: None
Are there multiple versions of the dataset? No A. If yes, name of file(s) that was updated: NA i. Why was the file updated? NA ii. When was the file updated? NA

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Data specific information for: age_size.rda

These data are derived from NOAA California Cooperative Oceanic Fisheries Investigations cruises in the Southern California Bight from 1998-2013. They contain collection information, genetic species identification, larval rockfish body and otolith measurements.

Number of variables: 13
Number of cases/rows: 1502
Variable List: *Year: Year larval rockfish were collected (YYYY) *Month: Month larval rockfish were collected (M) *species: Rockfish species (goodei, hopkinsi, jordani, mystinus, paucispinis, rufus, serranoides, wilsoni) *age: larval rockfish age (days) *rad1: radius to age 1 otolith increment (mm) *rad2: radius to age 2 otolith increment (mm) *TL.mm: Total length (mm) *Line_station: Name of the station where each fish was collected *lat: latitude (decimal degrees) *lon: longitude (decimal degrees) *µm_core: otolith nuclear radius (µm) *µm_last2: width of last two otolith growth increments (µm) *inc_1: first increment width (µm)
Missing data codes: "NA" (data not available)
Specialized formats or other abbreviations used: None

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Data specific information for: calcofi stations with date and time 98-13.csv

These data contain date and time of the rockfish collections at each station.

Number of variables: 17
Number of cases/rows: 4136
Variable List: calcofi stations with date and time 98-13.csv *unique.code2: code tying each collection to the cruise name and order of occupancy *unique.code: code tying each station to the line, order of occupancy, cruise, and ship *S_C: cruise name *S_SC: ship *Line: name of the transect (line) being sampled *Station: name of a station on a given line being sampled *longitude: decimal degrees *latitude: decimal degrees *season: season sampled (winter, spring, summer, fall) *Line_station: identifier of location sampled that includes both the line and station *S_OO: station order of occupancy on a given cruise *date: (M/DD/YY) *time: (YYYY-MM-DD time in GMT) *Month: (M) *day: day in a given month (D) *Year: (YYYY) *Jday: Day of year
Missing data codes: "NA" (data not available)
Specialized formats or other abbreviations used: None

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DATA-SPECIFIC INFORMATION FOR: Fall_OC_growth_ENV_PSUW.rda

These data are used to run a partial least squares regression analyses for each species to examine how oceanographic conditions female rockfish experience in fall, during gestion, affect the quality of the larvae they produce in winter. These data have mean otolith characteristics averaged for each species at a given station in a given year combined with the fall oceanographic conditions at basin, regional, and station/depth specific level for each species.

Number of variables: 23
Number of cases/rows: 583
Variable List: *Station: name of a station on a given line being sampled *Line: name of the transect (line) being sampled *Year_larva: year larva was collected (YYYY) *Year_mom: year that fall oceanographic conditions were sampled to capture maternal oceanographic experience (YYYY) *species: Rockfish species (goodei, hopkinsi, jordani, mystinus, paucispinis, rufus, serranoides, wilsoni) *mean_core: mean otolith core width averaged for each species at a given station in a given year (µm) *mean_distance: distance from nearest fishing port (km) *Year: year (YYYY) that oceanographic conditions were sampled (same as Year_mom) *avgBEUTI: Biologically effective upwelling transport index (BEUTI see Jacox et al. 2018. Coastal upwelling revisted: Ekman, Bakun, and improved upwelling indices for the U.S. west coast) *avgONI: Ocean Nino Index (ONI a basin scale measurement of sea surface temperature) *avgPDO: Pacific Decadal Oscillation (PDO a measure of low-frequency sea surface temperature variability throughout the northeast Pacific) *avgNPGO: North Pacific Gyre Oscillation (NPGO an index of the strength of equatorward flow of the California Current, vertical mixing, and surface salinity, nutrient,and chlorophyll concentrations in the southern CCLME) *avgwind: Meridional wind calculated for the southern Californa Bight. *spice_25.5: Spiciness (is a state variable and is derived from temperature and salinity, with lower spice values characteristic of cooler, fresher waters) calculated along the 25.5 potential density isopycnal layer. *x_PSUW_25.5: Percent Pacific Subrctic Upper Water at the 25.5 potential density isopycnal layer. (PSUW relative contribution of this watermass at a given CTD station. PSUW is characterized as low in temperatuer and salinity, high in O2, and nutrient rich) *spice_25.8: Spiciness calculated along the 25.8 potential density isopycnal layer. *x_PSUW_25.8: PSUW calculated along the 25.8 potential density isopycnal layer. *spice_26.1: Spiciness calculated along the 26.1 potential density isopycnal layer. *x_PSUW_26.1: PSUW calculated along the 26.1 potential density isopycnal layer. *spice_26.5: Spiciness calculated along the 26.5 potential density isopycnal layer. *x_PSUW_26.5: PSUW calculated along the 26.5 potential density isopycnal layer. *spice_26.8: Spiciness calculated along the 26.8 potential density isopycnal layer. *x_PSUW_26.8: PSUW calculated along the 26.1 potential density isopycnal layer.
Missing data codes: "NA" (data not available)
Specialized formats or other abbreviations used: None

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DATA-SPECIFIC INFORMATION FOR: winter_OC_age_ENV_PSUW.rda

These data are used to run a partial least squares regression analyses for each species to examine how a combination of maternal investment and the oceanographic conditions larval rockfish experience in winter after they have been extruded affect their survival (using age as a proxy for survival). These data have mean otolith characteristics averaged for each species at a given station in a given year combined with the winter oceanographic conditions at basin, regional, and station/depth specific level for each species.

Number of variables: 15
Number of cases/rows: 583
Variable List: *Station: name of a station on a given line being sampled *Line: name of the transect (line) being sampled *Year_larva: year larva was collected (YYYY) *Year_mom: year that fall oceanographic conditions were sampled to capture maternal oceanographic experience (YYYY) *species: Rockfish species (goodei, hopkinsi, jordani, mystinus, paucispinis, rufus, serranoides, wilsoni) *mean_age: mean age averaged for each species at a given station in a given year (days) *mean_core: mean otolith core width averaged for each species at a given station in a given year (µm) *mean_distance: distance from nearest fishing port (km) *Year: year (YYYY) that oceanographic conditions were sampled (same as Year_mom) *avgBEUTI: Biologically effective upwelling transport index (BEUTI see Jacox et al. 2018. Coastal upwelling revisted: Ekman, Bakun, and improved upwelling indices for the U.S. west coast) *avgONI: Ocean Nino Index (ONI a basin scale measurement of sea surface temperature) *avgPDO: Pacific Decadal Oscillation (PDO a measure of low-frequency sea surface temperature variability throughout the northeast Pacific) *avgNPGO: North Pacific Gyre Oscillation (NPGO an index of the strength of equatorward flow of the California Current, vertical mixing, and surface salinity, nutrient,and chlorophyll concentrations in the southern CCLME) *avgwind: Meridional wind calculated for the southern Californa Bight. *spice_25.5: Spiciness (is a state variable and is derived from temperature and salinity, with lower spice values characteristic of cooler, fresher waters) calculated along the 25.5 potential density isopycnal layer. *x_PSUW_25.5: Percent Pacific Subrctic Upper Water at the 25.5 potential density isopycnal layer. (PSUW relative contribution of this watermass at a given CTD station. PSUW is characterized as low in temperatuer and salinity, high in O2, and nutrient rich) *spice_25.8: Spiciness calculated along the 25.8 potential density isopycnal layer. *x_PSUW_25.8: PSUW calculated along the 25.8 potential density isopycnal layer.
Missing data codes: "NA" (data not available)
Specialized formats or other abbreviations used: None

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DATA-SPECIFIC INFORMATION FOR: Mean_winter_OC_dist_growth_resid_goodei_ENV_PSUW.rda
These data are used to run a partial least squares regression analyses for Sebastes goodei to examine how a combination of maternal investment and the oceanographic conditions larval rockfish experience in winter after they have been extruded affect their age corrected recent growth. These data have mean otolith characteristics averaged for each species at a given station in a given year combined with the winter oceanographic conditions at basin, regional, and station/depth specific level for each species.

Number of variables: 17
Number of cases/rows: 28
Variable List: *Station: name of a station on a given line being sampled *Line: name of the transect (line) being sampled *Year_larva: year larva was collected (YYYY) *Year_mom: year that fall oceanographic conditions were sampled to capture maternal oceanographic experience (YYYY) *species: Rockfish species (goodei) *mean_resid: mean recent growth-at-age residual for S. goodei averaged at each station in a given year *mean_age: mean age averaged for each species at a given station in a given year (days) *mean_core: mean otolith core width averaged for each species at a given station in a given year (µm) *mean_distance: distance from nearest fishing port (km) *Year: year (YYYY) that oceanographic conditions were sampled (same as Year_mom) *avgBEUTI: Biologically effective upwelling transport index (BEUTI see Jacox et al. 2018. Coastal upwelling revisted: Ekman, Bakun, and improved upwelling indices for the U.S. west coast) *avgONI: Ocean Nino Index (ONI a basin scale measurement of sea surface temperature) *avgPDO: Pacific Decadal Oscillation (PDO a measure of low-frequency sea surface temperature variability throughout the northeast Pacific) *avgNPGO: North Pacific Gyre Oscillation (NPGO an index of the strength of equatorward flow of the California Current, vertical mixing, and surface salinity, nutrient,and chlorophyll concentrations in the southern CCLME) *avgwind: Meridional wind calculated for the southern Californa Bight. *spice_25.8: Spiciness calculated along the 25.8 potential density isopycnal layer. *x_PSUW_25.8: PSUW calculated along the 25.8 potential density isopycnal layer.
Missing data codes: "NA" (data not available)
Specialized formats or other abbreviations used: None

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DATA-SPECIFIC INFORMATION FOR: Mean_winter_OC_dist_growth_resid_hopkinsi_ENV_PSUW.rda
These data are used to run a partial least squares regression analyses for Sebastes hopkinsi to examine how a combination of maternal investment and the oceanographic conditions larval rockfish experience in winter after they have been extruded affect their age corrected recent growth. These data have mean otolith characteristics averaged for each species at a given station in a given year combined with the winter oceanographic conditions at basin, regional, and station/depth specific level for each species.

Number of variables: 17
Number of cases/rows: 57
Variable List: *Station: name of a station on a given line being sampled *Line: name of the transect (line) being sampled *Year_larva: year larva was collected (YYYY) *Year_mom: year that fall oceanographic conditions were sampled to capture maternal oceanographic experience (YYYY) *species: Rockfish species (hopkinsi) *mean_resid: mean recent growth-at-age residual for S. hopkinsi averaged at each station in a given year *mean_age: mean age averaged for each species at a given station in a given year (days) *mean_core: mean otolith core width averaged for each species at a given station in a given year (µm) *mean_distance: distance from nearest fishing port (km) *Year: year (YYYY) that oceanographic conditions were sampled (same as Year_mom) *avgBEUTI: Biologically effective upwelling transport index (BEUTI see Jacox et al. 2018. Coastal upwelling revisted: Ekman, Bakun, and improved upwelling indices for the U.S. west coast) *avgONI: Ocean Nino Index (ONI a basin scale measurement of sea surface temperature) *avgPDO: Pacific Decadal Oscillation (PDO a measure of low-frequency sea surface temperature variability throughout the northeast Pacific) *avgNPGO: North Pacific Gyre Oscillation (NPGO an index of the strength of equatorward flow of the California Current, vertical mixing, and surface salinity, nutrient,and chlorophyll concentrations in the southern CCLME) *avgwind: Meridional wind calculated for the southern Californa Bight. *spice_25.8: Spiciness calculated along the 25.8 potential density isopycnal layer. *x_PSUW_25.8: PSUW calculated along the 25.8 potential density isopycnal layer.
Missing data codes: "NA" (data not available)
Specialized formats or other abbreviations used: None

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DATA-SPECIFIC INFORMATION FOR: Mean_winter_OC_dist_growth_resid_jordani_ENV_PSUW.rda
These data are used to run a partial least squares regression analyses for Sebastes jordani to examine how a combination of maternal investment and the oceanographic conditions larval rockfish experience in winter after they have been extruded affect their age corrected recent growth. These data have mean otolith characteristics averaged for each species at a given station in a given year combined with the winter oceanographic conditions at basin, regional, and station/depth specific level for each species.

Number of variables: 17
Number of cases/rows: 58
Variable List: *Station: name of a station on a given line being sampled *Line: name of the transect (line) being sampled *Year_larva: year larva was collected (YYYY) *Year_mom: year that fall oceanographic conditions were sampled to capture maternal oceanographic experience (YYYY) *species: Rockfish species (jordani) *mean_resid: mean recent growth-at-age residual for S. jordani averaged at each station in a given year *mean_age: mean age averaged for each species at a given station in a given year (days) *mean_core: mean otolith core width averaged for each species at a given station in a given year (µm) *mean_distance: distance from nearest fishing port (km) *Year: year (YYYY) that oceanographic conditions were sampled (same as Year_mom) *avgBEUTI: Biologically effective upwelling transport index (BEUTI see Jacox et al. 2018. Coastal upwelling revisted: Ekman, Bakun, and improved upwelling indices for the U.S. west coast) *avgONI: Ocean Nino Index (ONI a basin scale measurement of sea surface temperature) *avgPDO: Pacific Decadal Oscillation (PDO a measure of low-frequency sea surface temperature variability throughout the northeast Pacific) *avgNPGO: North Pacific Gyre Oscillation (NPGO an index of the strength of equatorward flow of the California Current, vertical mixing, and surface salinity, nutrient,and chlorophyll concentrations in the southern CCLME) *avgwind: Meridional wind calculated for the southern Californa Bight. *spice_25.8: Spiciness calculated along the 25.8 potential density isopycnal layer. *x_PSUW_25.8: PSUW calculated along the 25.8 potential density isopycnal layer.
Missing data codes: "NA" (data not available)
Specialized formats or other abbreviations used: None

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DATA-SPECIFIC INFORMATION FOR: Mean_winter_OC_dist_growth_resid_mystinus_ENV_PSUW.rda
There were insufficient samples to run this analysis for S. mystinus.

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DATA-SPECIFIC INFORMATION FOR: Mean_winter_OC_dist_growth_resid_paucispinis_ENV_PSUW.rda
These data are used to run a partial least squares regression analyses for Sebastes paucispinis to examine how a combination of maternal investment and the oceanographic conditions larval rockfish experience in winter after they have been extruded affect their age corrected recent growth. These data have mean otolith characteristics averaged for each species at a given station in a given year combined with the winter oceanographic conditions at basin, regional, and station/depth specific level for each species.

Number of variables: 17
Number of cases/rows: 29
Variable List: *Station: name of a station on a given line being sampled *Line: name of the transect (line) being sampled *Year_larva: year larva was collected (YYYY) *Year_mom: year that fall oceanographic conditions were sampled to capture maternal oceanographic experience (YYYY) *species: Rockfish species (paucispinis) *mean_resid: mean recent growth-at-age residual for S. paucispinis averaged at each station in a given year *mean_age: mean age averaged for each species at a given station in a given year (days) *mean_core: mean otolith core width averaged for each species at a given station in a given year (µm) *mean_distance: distance from nearest fishing port (km) *Year: year (YYYY) that oceanographic conditions were sampled (same as Year_mom) *avgBEUTI: Biologically effective upwelling transport index (BEUTI see Jacox et al. 2018. Coastal upwelling revisted: Ekman, Bakun, and improved upwelling indices for the U.S. west coast) *avgONI: Ocean Nino Index (ONI a basin scale measurement of sea surface temperature) *avgPDO: Pacific Decadal Oscillation (PDO a measure of low-frequency sea surface temperature variability throughout the northeast Pacific) *avgNPGO: North Pacific Gyre Oscillation (NPGO an index of the strength of equatorward flow of the California Current, vertical mixing, and surface salinity, nutrient,and chlorophyll concentrations in the southern CCLME) *avgwind: Meridional wind calculated for the southern Californa Bight. *spice_25.8: Spiciness calculated along the 25.8 potential density isopycnal layer. *x_PSUW_25.8: PSUW calculated along the 25.8 potential density isopycnal layer.
Missing data codes: "NA" (data not available)
Specialized formats or other abbreviations used: None

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DATA-SPECIFIC INFORMATION FOR: Mean_winter_OC_dist_growth_resid_rufus_ENV_PSUW.rda
These data are used to run a partial least squares regression analyses for Sebastes rufus to examine how a combination of maternal investment and the oceanographic conditions larval rockfish experience in winter after they have been extruded affect their age corrected recent growth. These data have mean otolith characteristics averaged for each species at a given station in a given year combined with the winter oceanographic conditions at basin, regional, and station/depth specific level for each species.

Number of variables: 17
Number of cases/rows: 31
Variable List: *Station: name of a station on a given line being sampled *Line: name of the transect (line) being sampled *Year_larva: year larva was collected (YYYY) *Year_mom: year that fall oceanographic conditions were sampled to capture maternal oceanographic experience (YYYY) *species: Rockfish species (rufus) *mean_resid: mean recent growth-at-age residual for S. rufus averaged at each station in a given year *mean_age: mean age averaged for each species at a given station in a given year (days) *mean_core: mean otolith core width averaged for each species at a given station in a given year (µm) *mean_distance: distance from nearest fishing port (km) *Year: year (YYYY) that oceanographic conditions were sampled (same as Year_mom) *avgBEUTI: Biologically effective upwelling transport index (BEUTI see Jacox et al. 2018. Coastal upwelling revisted: Ekman, Bakun, and improved upwelling indices for the U.S. west coast) *avgONI: Ocean Nino Index (ONI a basin scale measurement of sea surface temperature) *avgPDO: Pacific Decadal Oscillation (PDO a measure of low-frequency sea surface temperature variability throughout the northeast Pacific) *avgNPGO: North Pacific Gyre Oscillation (NPGO an index of the strength of equatorward flow of the California Current, vertical mixing, and surface salinity, nutrient,and chlorophyll concentrations in the southern CCLME) *avgwind: Meridional wind calculated for the southern Californa Bight. *spice_25.8: Spiciness calculated along the 25.8 potential density isopycnal layer. *x_PSUW_25.8: PSUW calculated along the 25.8 potential density isopycnal layer.
Missing data codes: "NA" (data not available)
Specialized formats or other abbreviations used: None

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DATA-SPECIFIC INFORMATION FOR: Mean_winter_OC_dist_growth_resid_serranoides_ENV_PSUW.rda
These data are used to run a partial least squares regression analyses for Sebastes serranoides to examine how a combination of maternal investment and the oceanographic conditions larval rockfish experience in winter after they have been extruded affect their age corrected recent growth. These data have mean otolith characteristics averaged for each species at a given station in a given year combined with the winter oceanographic conditions at basin, regional, and station/depth specific level for each species.

Number of variables: 17
Number of cases/rows: 11
Variable List: *Station: name of a station on a given line being sampled *Line: name of the transect (line) being sampled *Year_larva: year larva was collected (YYYY) *Year_mom: year that fall oceanographic conditions were sampled to capture maternal oceanographic experience (YYYY) *species: Rockfish species (serranoides) *mean_resid: mean recent growth-at-age residual for S. serranoides averaged at each station in a given year *mean_age: mean age averaged for each species at a given station in a given year (days) *mean_core: mean otolith core width averaged for each species at a given station in a given year (µm) *mean_distance: distance from nearest fishing port (km) *Year: year (YYYY) that oceanographic conditions were sampled (same as Year_mom) *avgBEUTI: Biologically effective upwelling transport index (BEUTI see Jacox et al. 2018. Coastal upwelling revisted: Ekman, Bakun, and improved upwelling indices for the U.S. west coast) *avgONI: Ocean Nino Index (ONI a basin scale measurement of sea surface temperature) *avgPDO: Pacific Decadal Oscillation (PDO a measure of low-frequency sea surface temperature variability throughout the northeast Pacific) *avgNPGO: North Pacific Gyre Oscillation (NPGO an index of the strength of equatorward flow of the California Current, vertical mixing, and surface salinity, nutrient,and chlorophyll concentrations in the southern CCLME) *avgwind: Meridional wind calculated for the southern Californa Bight. *spice_25.8: Spiciness calculated along the 25.8 potential density isopycnal layer. *x_PSUW_25.8: PSUW calculated along the 25.8 potential density isopycnal layer.
Missing data codes: "NA" (data not available)
Specialized formats or other abbreviations used: None

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DATA-SPECIFIC INFORMATION FOR: Mean_winter_OC_dist_growth_resid_wilsoni_ENV_PSUW.rda
These data are used to run a partial least squares regression analyses for Sebastes wilsoni to examine how a combination of maternal investment and the oceanographic conditions larval rockfish experience in winter after they have been extruded affect their age corrected recent growth. These data have mean otolith characteristics averaged for each species at a given station in a given year combined with the winter oceanographic conditions at basin, regional, and station/depth specific level for each species.

Number of variables: 17
Number of cases/rows: 45
Variable List: *Station: name of a station on a given line being sampled *Line: name of the transect (line) being sampled *Year_larva: year larva was collected (YYYY) *Year_mom: year that fall oceanographic conditions were sampled to capture maternal oceanographic experience (YYYY) *species: Rockfish species (wilsoni) *mean_resid: mean recent growth-at-age residual for S. wilsoni averaged at each station in a given year *mean_age: mean age averaged for each species at a given station in a given year (days) *mean_core: mean otolith core width averaged for each species at a given station in a given year (µm) *mean_distance: distance from nearest fishing port (km) *Year: year (YYYY) that oceanographic conditions were sampled (same as Year_mom) *avgBEUTI: Biologically effective upwelling transport index (BEUTI see Jacox et al. 2018. Coastal upwelling revisted: Ekman, Bakun, and improved upwelling indices for the U.S. west coast) *avgONI: Ocean Nino Index (ONI a basin scale measurement of sea surface temperature) *avgPDO: Pacific Decadal Oscillation (PDO a measure of low-frequency sea surface temperature variability throughout the northeast Pacific) *avgNPGO: North Pacific Gyre Oscillation (NPGO an index of the strength of equatorward flow of the California Current, vertical mixing, and surface salinity, nutrient,and chlorophyll concentrations in the southern CCLME) *avgwind: Meridional wind calculated for the southern Californa Bight. *spice_25.8: Spiciness calculated along the 25.8 potential density isopycnal layer. *x_PSUW_25.8: PSUW calculated along the 25.8 potential density isopycnal layer.
Missing data codes: "NA" (data not available)
Specialized formats or other abbreviations used: None

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Data specific information for: rockfish_age.rda

These data contain date and time of the rockfish collections at each station.

Number of variables: 16
Number of cases/rows: 1502
Variable List: calcofi stations with date and time 98-13.csv *Line: name of the transect (line) being sampled *Station: name of a station on a given line being sampled *Line_station: identifier of location sampled that includes both the line and station *latitude: decimal degrees *longitude: decimal degrees *Year: (YYYY) *Month.x: (M) *species: Rockfish species (goodei, hopkinsi, jordani, mystinus, paucispinis, rufus, serranoides, wilsoni) *age: larval rockfish age (days) *µm_core: otolith nuclear radius (µm) *µm_last2: width of last two otolith growth increments (µm) *date: (M/DD/YYYY) *time: (YYYY-MM-DD time in GMT) *day: day in a given month (d) *Jday: Day of year (D) *DOB: Date of birth (D)
Missing data codes: "NA" (data not available)
Specialized formats or other abbreviations used: None

Methods

Sample collection

Rockfish larvae were collected during winter CalCOFI cruises from 1998 to 2013 as described in Thompson et al. (2017). Winter cruises take place in January-February with the majority (72–98%) of larval rockfish collected in January (Table 1). Bongo nets were deployed at fixed stations to 210 m and obliquely towed to the surface at a constant rate (Kramer 1972; Figure 1). Plankton from the port-side net was initially preserved in 95% ethanol and changed for fresh 95% ethanol after 24 hours. In the laboratory, rockfish larvae were sorted and enumerated from stations over the continental shelf (inside yellow polygon figure 1). Because most rockfish larvae are not morphologically distinguishable to the species level, the mitochondrial cytochrome b gene was sequenced from each individual larva using DNA extracted from rockfish tissue (see Thompson et al. 2017 for details on sequencing), and identities were determined by comparing larval sequence to reference sequences from adults (64). After sequencing, larvae were stored individually in vials filled with 100% ethanol.

Rockfish early life history trait measurement

We focused our analysis on eight rockfish species found throughout the Southern California Bight. Five of the species are commercially/recreationally fished (S. goodei, S. mystinus, S. paucispinis, S. rufus, S. serranoides) and three are non-targeted (S. hopkinsi, S. jordani, S. wilsoni), although these non-targets species are occasionally caught as bycatch in other fisheries. A total of 5,475 individuals from all 8 target species were collected between 1998–2013. Of those, 2021 were selected for otolith extraction (a maximum of 20 larvae from each species per year). Larvae were placed in a drop of deionized water on a microscope slide under a dissecting microscope and basic morphometrics, including total length, were recorded. Sagittal otoliths were then extracted from each fish using micro-forceps and insect mounting pins. The otoliths were affixed whole to microscope slides with a drop of clear fingernail polish. Polishing was not necessary, as intact otoliths from larvae (< 20 mm TL) had discernable growth increments with no further preparation.

Otoliths were photographed using a DSLR camera (Nikon D7000) mounted to a compound microscope (Leica DMLB) at 1000× magnification. Images were analyzed in R using the RFishBC package (v0.2.4; Ogle 2022). This package facilitates measuring otolith increment widths and estimating ages by applying a known scale to defined measurements made on collected images. Otolith images were batched and analyzed by year and species. Otolith core width-at-extrusion (hereafter otolith core width) was measured from the center of the core to the postrostral edge of the extrusion check (a mark in the otolith that forms when the larva is released from the mother). Ages were obtained by increment counts beginning at the first growth increment after the extrusion check. For quality control, a randomized sub-sample of images was examined by an experienced reader twice, with an extended time interval between reads. If age estimates differed between the first two reads, the otolith photographs were examined for a third time. Samples were not used in further analyses if the third reading did not agree with one of the first two. Of the 2,021 otoliths aged, 1,502 had agreement between reads, and 1,499 were used for this study (3 individuals were collected in offshore stations outside of the region of study; Table 1). Growth increments were not validated during this study. However, these counts were assumed to correspond to daily ages because the formation of daily growth increments has been validated for several of these species, including S. jordani (66), S. paucispinis, and S. goodei (67).

Oceanographic conditions & Source-water analysis

We gathered a suite of oceanographic data from basin, regional, and station scales to characterize the oceanographic conditions pregnant female rockfishes and larval rockfishes experienced. Based on previous work (Schroeder et al. 2018), we hypothesized that the conditions females experience may play an important role in determining larval quality. At the basin scale, we included the Pacific Decadal Oscillation (PDO), a measure of low-frequency sea surface temperature variability throughout the northeast Pacific, the Ocean Niño Index (ONI), which measures equatorial upper water temperature and is an indicator of El Niño Southern Oscillation State, and the North Pacific Gyre Oscillation (NPGO), an index of the strength of equatorward flow of the California Current, vertical mixing, and surface salinity, nutrient, and chlorophyll concentrations in the southern CCLME (68). Regional oceanographic variables included two measures of wind-driven upwelling intensity: the Biologically Effective Upwelling Transport Index (BEUTI; Jacox et al. 2018) at 33°N, and meridional winds at 33.7°N and 119.1°W (from NOAA buoy 46025). At the local scale of the CalCOFI stations where rockfish were collected, we calculated the distance to the nearest fishing port (also a proxy for distance to shore) and two indicators of the source waters contributing to water column characteristics: the PSUW fraction and Spiciness (Schroeder et al. 2018). Spiciness is a state variable and is derived from temperature and salinity, with lower spice values characteristic of cooler, fresher waters (Flament 2002). Water-mass fraction, at each CalCOFI station and in the upper 500 m, is obtained from an optimal multiparameter (OMP) analysis of 3 water masses that comprise upper waters in the CCS (Bograd et al. 2019). Spiciness has been used to describe changes in interannual variability of rockfish recruitment as abundances of pelagic juveniles (the index of recruitment in stock assessments; e.g., He and Field 2017) were higher for most species during years with low spiciness (Schroeder et al. 2018). An OMP analysis, using CalCOFI hydrographic data starting from 1984, quantifies the mixing between PSUW, Eastern North Pacific Central Water (ENPCW), and Pacific Equatorial Water (PEW) water masses (Bograd et al. 2019). Of the three water masses used in the OMP analysis, PSUW is the water mass of subarctic origin that is advected into the CCE, with the greatest percentages occurring below 100 m. PSUW has the lowest spiciness values, and we used the PSUW fraction in our analyses. Spice and PSUW fraction have been calculated for all CalCOFI stations used in this study at 5 m depth intervals from the surface to 500 m. Profiles of spice and PSUW fraction were linearly interpolated on 1 m intervals and values are extracted on isopycnals σθ = 25.5, 25.8, 26.1, 26.5, 26.8 kg/m³ covering depths ranging between 50 m to 400 m. We report PSUW fraction as a percentage (PSUW%) at a given time (season and year), station, and depth. The combination of all three water masses (PSUW, ENPCW, and PEW) will equal to 1. OMP analysis has been calculated for all quarterly CalCOFI surveys, however, for this study, only the fall and winter quarters are considered to align with rockfish gestation in fall and larval rockfish early life in winter.

Data analysis

To determine whether the otolith core width provided a proxy for larval fish size-at-extrusion, as has been demonstrated in other species (Garrido et al. 2015), we used linear regression to examine the amount of variability in length of all one-day-old rockfish larvae explained by otolith core width. While we didn’t have immediately-extruded (day 0) larvae available, we assumed that one-day-old larvae provided an accurate representation of larval length-at-extrusion.

We examined the relationship between timing of extrusion and otolith core width to determine if core size was influenced by when larvae were extruded as there is evidence that older, larger females reproduce earlier in the reproductive season. We again used linear regression with date of extrusion as our explanatory variable to test this relationship.

We evaluated time series of annual, species-specific, average anomalies of larval rockfish early life history traits to determine if patterns of otolith core width, recent growth, and age-at-capture were consistent across species (Figure S1). A time series of life history trait anomalies was calculated by taking the spatial average of each trait at all stations for each year and species, then subtracting a long-term mean of each trait from the annual values. We used Spearman’s rank correlation to evaluate the degree of correlation among species for each life history trait (Figures S2–4). Additionally, we plotted spatially averaged otolith core width size across the entire time series, at each station, and for each species to explore the spatial patterns of variability in otolith core width (Fig. 2).

Because we expected interannual and spatial variability in maternal and larval oceanographic experience, we calculated the mean core width size for each species at each station in each year and used partial least squares regression (PLSR; Carrascal et al. 2009) analysis with a suite of basin scale, regional, and local oceanographic conditions to understand the environmental drivers of otolith core width size. All environmental variables, except PSUW% and Spiciness, were averaged from September to December to capture the fall conditions adult female rockfish experienced while they were gestating. Fall PSUW% and spiciness were calculated from fall CalCOFI hydrographic data and were calculated along isopycnal layers (25.5, 25.8, 26.1, 26.5, 26.8) that were matched to the adult depth range of the different rockfish species.

PLSR was used to determine how oceanographic conditions and maternal investment contribute to larval rockfish recent growth rate and survival. Recent growth anomalies were calculated by taking the residuals of the relationship between mean growth of the last two growth increments and age-at-collection for each larva. Age-at-capture was used as a proxy for larval survival because mortality is high during this early period; years with older mean ages indicate higher larval survival (Garrido et al. 2015). We included the same environmental variables as in the core width analysis but averaged these from January to February (winter CalCOFI hydrographic surveys for PSUW and Spice) to capture the conditions larval rockfish experienced during early life before collection in winter CalCOFI cruises. As larval rockfish are typically found in the upper 80m (72) we used PSUW% and Spiciness on the 25.8 isopycnal, which is approximately 60 m deep near shore and 90 m deep offshore. We also included mean core width for each species at each station and year to examine the influence of larval size at extrusion on growth and survival. Similar to the calculation of mean core width, we calculated the mean recent growth rate, and mean age at each station in each year.

In each PLSR analysis we calculated the weight squared of each predictor variable to determine the relative contribution of each variable to the PLSR components. When the weights of each variable are squared, they sum to one, providing the percent contribution of each variable to the PLSR component. We used a cutoff of PLSR weight² > 0.1 to identify variables that contributed significantly (more than 10%) to the first PLSR component and drivers of variability in maternal investment, larval growth rate, and age-at-capture. All otolith analyses were performed in R (v4.1.2; R Core Team 2021)) using packages dplyr and plsrdepot. Figures were generated using R package ggplot2.

Momma's larvae: Maternal oceanographic experience and larval size influence early survival of rockfishes

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Abstract

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Methods

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