DOI: 10.5061/dryad.kh18932hn
title: Downscaled climate projections of future mesopelagic habitat in the California Current Ecosystem

description: Although the mesopelagic zone occupies a substantial volume of the
 world's oceans, our results suggest that the livable portion may
 compress vertically by ~40 m or ~39% by the end of the century. Using an
 ensemble of three downscaled climate projections from a high emissions
 scenario, we evaluated the connection between anthropogenic greenhouse gas
 emissions and changes in light and oxygen at depth, which influence the
 upper and lower limits of mesopelagic habitat in the central California
 Current. Although the model projects a small deepening (~ 2 m) of the
 upper light boundary consistent with increased stratification and reduced
 upper ocean productivity, the main driver of vertical mesopelagic habitat
 compression is the significant shoaling (by ~44 m) of the hypoxic boundary
 over the course of the 21st century. Differences in dissolved oxygen
 across ensemble members highlight the potential influence of equatorial
 dynamics and the California Undercurrent in constraining the future
 availability of mesopelagic habitat along the U.S. West Coast. Mesopelagic
 ecosystems connect the surface ocean to the deep sea, and a projected
 decrease in the vertical extent of mesopelagic habitat could have
 cascading effects on a broader range of marine ecosystem processes and
 carbon export.
description: <strong>Downscaled Regional Climate
 Projections</strong> We use an ensemble of
 high-resolution regional climate projections representing three different
 rates of warming under the RCP 8.5 high emissions scenario for the period
 2000-2100. The earth system model solutions are first downscaled to 1/10°
 (~10 km) resolution for the broader California Current (30-48
 °N)<sup>1,2</sup> and subsequently nested at 1/30° (~3 km)
 resolution for the central California Current (32-44 °N) to improve the
 representation of local scale coastal upwelling
 processes<sup>3</sup>. In this approach, the 1/10° downscaled
 projections are forced directly by the CMIP5 earth system models using a
 time-varying delta method, and the high-resolution nested projections are
 subsequently forced by the downscaled projections using an offline nesting
 method (Fig. 1). The three earth system model solutions selected here are
 GFDL-ESM2M, IPSLCM5, and Hadley-GEM2-E as they include marine
 biogeochemical fields and represent the spread of the CMIP5 ensemble
 (GFDL-ESM2M = low rate of warming; IPSLCM5 = rate of warming close to
 ensemble mean; Hadley-GEM2-E = high rate of warming). While the RCP8.5
 scenario may arguably depict an “unrealistically” warm future, we consider
 it useful here for two reasons: (1) it allowed exploring changes in
 mesopelagic habitat properties under extreme warming (e.g., identify
 potential thresholds), and (2) the lowest rate of warming (GFDL-ESM2M) is
 representative of the high end of the more moderate RCP4.5
 scenario. The physical and biogeochemical fields for
 both downscaled (1/10°) and nested (1/30°) projections are generated using
 an implementation of the Regional Ocean Modeling System
 (ROMS)<sup>4,5</sup> for the California Current System coupled
 to NEMUCSC, a customized version of the North Pacific Ecosystem Model for
 Understanding Regional Oceanography (NEMURO)<sup>6</sup>.
 NEMUCSC includes three limiting macronutrients (nitrate, ammonium, and
 silicic acid), two phytoplankton functional groups (nanophytoplankton and
 diatoms), three zooplankton size-classes (microzooplankton, copepods, and
 euphausiids), three detritus pools (dissolved and particulate organic
 nitrogen and particulate silica), as well as carbon and oxygen
 cycling<sup>7,8</sup>. The three high-resolution nested
 projections of the coupled ROMS-NEMUCSC model are hereafter referred to as
 “ROMS-GFDL”, “ROMS-IPSL”, and “ROMS-HADL”.
 <strong>References</strong>
 1.         Pozo Buil, M. <em>et al.</em> A
 Dynamically Downscaled Ensemble of Future Projections for the California
 Current System. <em>Front. Mar. Sci.</em>
 <strong>8</strong>, 612874 (2021).
 2.         Fiechter, J., Pozo Buil, M., Jacox, M. G., Alexander,
 M. A. & Rose, K. A. Projected Shifts in 21st Century Sardine
 Distribution and Catch in the California Current. <em>Front. Mar.
 Sci.</em> <strong>8</strong>, 685241 (2021).
 3.         Fiechter, J., Edwards, C. A. & Moore, A. M.
 Wind, Circulation, and Topographic Effects on Alongshore Phytoplankton
 Variability in the California Current. <em>Geophys. Res.
 Lett.</em> <strong>45</strong>, 3238–3245
 (2018). 4.         Haidvogel, D. B. <em>et
 al.</em> Ocean forecasting in terrain-following coordinates:
 Formulation and skill assessment of the Regional Ocean Modeling System.
 <em>J. Comput. Phys.</em> <strong>227</strong>,
 3595–3624 (2008). 5.         Shchepetkin, A. F.
 & McWilliams, J. C. The regional oceanic modeling system (ROMS): a
 split-explicit, free-surface, topography-following-coordinate oceanic
 model. <em>Ocean Model.</em> <strong>9</strong>,
 347–404 (2005). 6.         Kishi, M. J. <em>et
 al.</em> NEMURO—a lower trophic level model for the North Pacific
 marine ecosystem. <em>Ecol. Model.</em>
 <strong>202</strong>, 12–25 (2007).
 7.         Fiechter, J., Santora, J. A., Chavez, F., Northcott,
 D. & Messié, M. Krill Hotspot Formation and Phenology in the
 California Current Ecosystem. <em>Geophys. Res. Lett.</em>
 <strong>47</strong>, e2020GL088039 (2020).
 8.         Cheresh, J. & Fiechter, J. Physical and
 Biogeochemical Drivers of Alongshore pH and Oxygen Variability in the
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 <strong>47</strong>, e2020GL089553 (2020).
description: # Downscaled climate projections of future mesopelagic habitat in the
 California Current Ecosystem
 [https://doi.org/10.5061/dryad.kh18932hn](https://doi.org/10.5061/dryad.kh18932hn) ## Description of the data and file structure The following oceanographic data and R code accompany the manuscript "Projected 21st century compression of mesopelagic habitat in the California Current" submitted to Scientific Reports. Using an ensemble of three high-resolution downscaled climate projections for the California Current under a high emissions scenario, we evaluated potential changes in the availability of mesopelagic habitat by the end of the 21st century. The upper and lower boundaries of the mesopelagic zone are defined as the depth at which light intensity reaches (0.0217 W/m2) and the depth of the hypoxic boundary defined as ~63 mmol/m3. Additional ocean metrics include: temperature at 150 m, dissolved oxygen at 300 m, Integrated chlorophyll in the upper 100 m, maximum buoyancy frequency (N^2) in upper 100 m, light intensity at 150 m and mean nitrate (NO3) in the upper 100m. ### Files and variables #### File: light.csv **Description:** Downscaled climate projections (2000-2100) of light metrics averaged over our study domain (see Figure 1 in manuscript). Ensemble mean and spread were calculated as the mean and standard deviation (sd) of the 3 projections from ROMS-GFDL, ROMS-IPSL and ROMS-HADL (see manuscript for full descriptions). ##### **Variables** * LIGHT_150_ENSEMBLE: Ensemble mean of light intensity (units of W/m^2) at a depth of 150 m. * LIGHT_150_ENSEMBLE_SD: Standard deviation (ensemble spread) of LIGHT_150_ENSEMBLE * LIGHT_150_GFDL: Spatial mean of light intensity at 150 m (2000-2100) from ROMS_GFDL * LIGHT_150_IPSL: Spatial mean of light intensity at 150 m (2000-2100) from ROMS_IPSL * LIGHT_150_HAD: Spatial mean of light intensity at 150 m (2000-2100) from ROMS_HAD * EUPHOTIC_DEPTH_ENSEMBLE: Ensemble mean of euphotic depth (light ~1% of surface) (units of m) * EUPHOTIC_DEPTH_ENSEMBLE_SD: Standard deviation (ensemble spread) of EUPHOTIC_DEPTH_ENSEMBLE * EUPHOTIC_DEPTH_GFDL: Spatial mean of euphotic depth (2000-2100) from ROMS_GFDL * EUPHOTIC_DEPTH_IPSL: Spatial mean of euphotic depth (2000-2100) from ROMS_IPSL * EUPHOTIC_DEPTH_HAD: Spatial mean of euphotic depth (2000-2100) from ROMS_HAD * DEPTH_LIGHT_REF_ENSEMBLE: Ensemble mean of the depth at which light reaches 0.0217 W/m2 (units of meters) * DEPTH_LIGHT_REF_ENSEMBLE_SD: Standard deviation (ensemble spread) of DEPTH_LIGHT_REF_ENSEMBLE * DEPTH_LIGHT_REF_GFDL: Spatial mean of reference light level depth (2000-2100) from ROMS_GFDL * DEPTH_LIGHT_REF_IPSL: Spatial mean of reference light level depth (2000-2100) from ROMS_IPSL * DEPTH_LIGHT_REF_HAD: Spatial mean of reference light level depth (2000-2100) from ROMS_HAD #### File: n2_no3_chl.csv **Description:** Downscaled climate projections (2000-2100) of oceanographic metrics averaged over our study domain (see Figure 1 in manuscript). Ensemble mean and spread were calculated as the mean and standard deviation (sd) of the 3 projections from ROMS-GFDL, ROMS-IPSL and ROMS-HADL (see manuscript for full descriptions). ##### **Variables** * N2_ENSEMBLE: Ensemble mean of max buoyancy frequency in upper 100 m (s^-1) * N2_ENSEMBLE_SD: Standard deviation (ensemble spread) of N2_ENSEMBLE * N2_GFDL: Spatial mean of max buoyancy frequency in upper 100 m (2000-2100) from ROMS_GFDL * N2_IPSL: Spatial mean of max buoyancy frequency in upper 100 m (2000-2100) from ROMS_IPSL * N2_HAD: Spatial mean of max buoyancy frequency in upper 100 m (2000-2100) from ROMS_HAD * CHL_100_ENSEMBLE: Ensemble mean of integrated chlorophyll in the upper 100 m (mg/m^3) * CHL_100_ENSEMBLE_SD: Standard deviation (ensemble spread) of CHL_100_ENSEMBLE * CHL_100_GFDL: Spatial mean of integrated chlorophyll in the upper 100 m (2000-2100) from ROMS_GFDL * CHL_100_IPSL: Spatial mean of integrated chlorophyll in the upper 100 m (2000-2100) from ROMS_IPSL * CHL_100_HAD: Spatial mean of integrated chlorophyll in the upper 100 m (2000-2100) from ROMS_HAD * NO3_100_ENSEMBLE: Ensemble mean of mean nitrate in the upper 100 m (mmol/m^3) * NO3_100_ENSEMBLE_SD: Standard deviation (ensemble spread) of NO3_100_ENSEMBLE * NO3_100_GFDL: Spatial mean of mean nitrate in the upper 100 m (2000-2100) from ROMS_GFDL * NO3_100_IPSL: Spatial mean of mean nitrate in the upper 100 m (2000-2100) from ROMS_IPSL * NO3_100_HAD: Spatial mean of mean nitrate in the upper 100 m (2000-2100) from ROMS_HAD #### File: oxygen.csv **Description:** Downscaled climate projections (2000-2100) of oxygen metrics averaged over our study domain (see Figure 1 in manuscript). Ensemble mean and spread were calculated as the mean and standard deviation (sd) of the 3 projections from ROMS-GFDL, ROMS-IPSL and ROMS-HADL (see manuscript for full descriptions). ##### **Variables** * DEPTH_OX_63_ENSEMBLE: Ensemble mean of hypoxic depth (63 mmol/m^3) (units of m) * DEPTH_OX_63_ENSEMBLE_SD: Standard deviation (ensemble spread) of DEPTH_OX_63_ENSEMBLE * DEPTH_OX_63_GFDL: Spatial mean of hypoxic depth (2000-2100) from ROMS_GFDL * DEPTH_OX_63_IPSL: Spatial mean of hypoxic depth (2000-2100) from ROMS_IPSL * DEPTH_OX_63_HAD: Spatial mean of hypoxic depth (2000-2100) from ROMS_HAD * OX_100_ENSEMBLE: Ensemble mean of dissolved oxygen at 100 m depth (units of mmol/m^3) * OX_100_ENSEMBLE_SD: Standard deviation (ensemble spread) of OX_100_ENSEMBLE * OX_200_ENSEMBLE: Ensemble mean of dissolved oxygen at 200 m depth (units of mmol/m^3) * OX_200_ENSEMBLE_SD: Standard deviation (ensemble spread) of OX_200_ENSEMBLE * OX_300_ENSEMBLE: Ensemble mean of dissolved oxygen at 300 m depth (units of mmol/m^3) * OX_300_ENSEMBLE_SD: Standard deviation (ensemble spread) of OX_300_ENSEMBLE * OX_300_GFDL: Spatial mean of hypoxic depth (2000-2100) from ROMS_GFDL * OX_300_IPSL: Spatial mean of hypoxic depth (2000-2100) from ROMS_IPSL * OX_300_HAD: Spatial mean of hypoxic depth (2000-2100) from ROMS_HAD * OX_400_ENSEMBLE: Ensemble mean of dissolved oxygen at 400 m depth (units of mmol/m^3) * OX_400_ENSEMBLE_SD: Standard deviation (ensemble spread) of OX_400_ENSEMBLE * OX_500_ENSEMBLE: Ensemble mean of dissolved oxygen at 500 m depth (units of mmol/m^3) * OX_500_ENSEMBLE_SD: Standard deviation (ensemble spread) of OX_500_ENSEMBLE #### File: temp_iso.csv **Description:** Downscaled climate projections (2000-2100) of temperature metrics averaged over our study domain (see Figure 1 in manuscript). Ensemble mean and spread were calculated as the mean and standard deviation (sd) of the 3 projections from ROMS-GFDL, ROMS-IPSL and ROMS-HADL (see manuscript for full descriptions). ##### **Variables** * TEMP_150_ENSEMBLE: Ensemble mean of temperature at 150 m depth (degrees C) * TEMP_150_ENSEMBLE_SD: Standard deviation (ensemble spread) of TEMP_150_ENSEMBLE * TEMP_150_GFDL: Spatial mean of temperature at 150 m (2000-2100) from ROMS_GFDL * TEMP_150_IPSL: Spatial mean of temperature at 150 m (2000-2100) from ROMS_IPSL * TEMP_150_HAD: Spatial mean of temperature at 150 m (2000-2100) from ROMS_HAD * DEPTH_ISO_26_5_ENSEMBLE: Ensemble mean of the depth of the 26.5 isopycnal (units of m) * DEPTH_ISO_26_5_ENSEMBLE_SD: Standard deviation (ensemble spread) of DEPTH_ISO_26_5_ENSEMBLE * DEPTH_ISO_26_5_GFDL: Spatial mean of isopycnal depth (2000-2100) from ROMS_GFDL * DEPTH_ISO_26_5_IPSL: Spatial mean of isopycnal depth (2000-2100) from ROMS_IPSL * DEPTH_ISO_26_5_HAD: Spatial mean of isopycnal depth (2000-2100) from ROMS_HAD #### File: meso_hab.csv **Description:** Downscaled climate projections (2000-2100) of mesopelagic habitat boundaries averaged over our study domain (see Figure 1 in manuscript). Ensemble mean and spread were calculated as the mean and standard deviation (sd) of the 3 projections from ROMS-GFDL, ROMS-IPSL and ROMS-HADL (see manuscript for full descriptions). ##### **Variables** * MESO_HABITAT_ENSEMBLE: Ensemble mean of the distance (in units of m) from the upper mesopelagic boundary (depth at which light = 0.0217 W/m2) above and hypoxic boundary depth (depth at which DO = 63 mmol/m3) below * MESO_HABITAT_ENSEMBLE_SD: Standard deviation (ensemble spread) of MESO_HABITAT_ENSEMBLE * MESO_HABITAT_GFDL: Spatial mean of vertical mesopelagic habitat extent (2000-2100) from ROMS_GFDL * MESO_HABITAT_IPSL: Spatial mean of mesopelagic habitat extent (2000-2100) from ROMS_IPSL * MESO_HABITAT_HAD: Spatial mean of mesopelagic habitat extent (2000-2100) from ROMS_HAD #### File: mesohabitat_proj_2000-2100.nc **Description:** High resolution downscaled climate projections. We used a 1/30° model domain nested within a set of existing downscaled regional climate projections at 1/10° resolution for the broader California Current region. Briefly, the regional projections downscale three earth system model solutions (GFDL-ESM2M, IPSLCM5, and Hadley-GEM2-E) representing the physical and biogeochemical spread of the CMIP5 ensemble under the RCP8.5 high emissions scenario. The three corresponding high-resolution downscaled projections are hereafter referred to as ROMS-GFDL, ROMS-IPSL, and ROMS-HADL and depict low (GFDL), moderate (IPSL), and high (HADL) rates of warming under RCP8.5. This .nc file contains variables used to characterize changes in the vertical extent of mesopelagic habitat for the central California Current: the upper light boundary depth, the lower hypoxic boundary depth and dissolved oxygen concentrations at 300 m depth over our spatial domain in the central California Current defined as the latitudes from 34.5 to 40, bottom depths &gt; 400 m and out to 200 km from the coastline. ##### **Variables** * depth_isolume_gfdl: the upper boundary of the mesopelagic zone, defined as the depth (in units of m) at which light intensity reaches 0.0217 W/m2. These data are high resolution downscaled climate projections (2000-2100) from ROMS-GFDL for our entire spatial domain (see Fig.1). * depth_isolume_ipsl: the upper boundary of the mesopelagic zone, defined as the depth (in units of m) at which light intensity reaches 0.0217 W/m2. These data are high resolution downscaled climate projections (2000-2100) from ROMS-IPSL for our entire spatial domain (see Fig.1). * depth_isolume_hadl: the upper boundary of the mesopelagic zone, defined as the depth (in units of m) at which light intensity reaches 0.0217 W/m2. These data are high resolution downscaled climate projections (2000-2100) from ROMS-HADL for our entire spatial domain (see Fig.1). * depth_hypoxic_gfdl: the lower boundary of the mesopelagic zone, defined as the depth (in units of m) at which dissolved oxygen reaches 63 mmol/m3 (hypoxic boundary). These data are high resolution downscaled climate projections (2000-2100) from ROMS-GFDL for our entire spatial domain (see Fig.1). * depth_hypoxic_ipsl: the lower boundary of the mesopelagic zone, defined as the depth (in units of m) at which dissolved oxygen reaches 63 mmol/m3 (hypoxic boundary). These data are high resolution downscaled climate projections (2000-2100) from ROMS-IPSL for our entire spatial domain (see Fig.1). * depth_hypoxic_hadl: the lower boundary of the mesopelagic zone, defined as the depth (in units of m) at which dissolved oxygen reaches 63 mmol/m3 (hypoxic boundary). These data are high resolution downscaled climate projections (2000-2100) from ROMS-HADL for our entire spatial domain (see Fig.1). * do_300m_gfdl: Concentration of dissolved oxygen (in units of mmol/m^3) at 300 m depth. These data are high resolution downscaled climate projections (2000-2100) from ROMS-GFDL for our entire spatial domain (see Fig.1). * do_300m_ipsl: Concentration of dissolved oxygen (in units of mmol/m^3) at 300 m depth. These data are high resolution downscaled climate projections (2000-2100) from ROMS-IPSL for our entire spatial domain (see Fig.1). * do_300m_hadl: Concentration of dissolved oxygen (in units of mmol/m^3) at 300 m depth. These data are high resolution downscaled climate projections (2000-2100) from ROMS-HADL for our entire spatial domain (see Fig.1). ## Code/software **Background**: The following code was written by II in the R language (R version 4.4.1 (2024-06-14) -- "Race for Your Life" Copyright (C) 2024 The R Foundation for Statistical Computing) using RStudio (Version 2024.09.0+375 (2024.09.0+375) Copyright (C) 2024 by Posit Software, PBC). To run this code, the five .csv files available from Dryad (light.csv, meso_hab.csv, n2_no3_chl.csv, oxygen.csv, temp_iso.csv) must be downloaded and stored in your current working directory under the folder name "roms." There is one RMarkdown file (Projections_analysis_R.Rmd) that provides code for analyzing model output. **Objectives of code files:** **Projections_analysis_R.Rmd** * Read in model output for oceanographic metrics and mesopelagic habitat boundary metrics * Create plots of the spatial mean of ensemble means and spread of oceanographic variables (temperature at 150 m, oxygen at 300 m, integrated chlorophyll in upper 100 m, max buoyancy frequency (in upper 100), light at 150 m, mean nitrate (NO3) in upper 100 m) from 2000-2100. * Create plot of changes in vertical mesopelagic habitat from 2000-2100 * Calculate summary statistics to describe changes in ocean conditions and mesopelagic habitat boundaries from the beginning (2000-2030) and end (2070-2100) of the century. ## Access information **Access information** Other publicly accessible locations of data used in this study: Our analysis also uses publicly available data available at: "A high-resolution synthesis dataset for multistressor analyses along the US West Coast" by Kennedy et al. 2024 ([https://doi.org/10.5194/essd-16-219-2024](https://doi.org/10.5194/essd-16-219-2024)).