DOI: 10.5061/dryad.7wm37pw3x
title: Selective breeding enhances coral heat tolerance even over small spatial scales

description: Coral reefs globally are experiencing escalating mass bleaching and
 mortality. Reefs along the western Indian Ocean have been relatively
 unimpacted. We assessed heat tolerance baselines in two widespread
 reef-building Acropora species and used selective breeding from two
 thermally distinct (present day and stress histories) northern (Mean
 Monthly Maximum 27.9 °C) and southern (26.6 °C) reefs along the Ningaloo
 World Heritage Reef. Fitness responses were measured in control and heat
 stress temperatures (adults = 31.0 °C, larvae = 35.5 °C), including
 survival, tissue necrosis, bleaching, and photosynthesis. Larvae with one
 parent from the warmer population exhibited &gt;2.2-fold higher
 survival under heat stress, while those with both parents from the warmer
 population survived 1.6-fold better (compared to control larvae with two
 parents from the cooler population). Photosynthesis was maintained in both
 species and both populations, suggesting heat responses were host driven.
 Adults from both populations from one species (A. tenuis) exhibited
 similar responses to heat, while the other (A. millepora) was more
 variable. These findings are the first to demonstrate that selective
 breeding can provide heat tolerance enhancement for corals in the Indian
 Ocean and will be critical to preparing for future marine heatwaves.
description: # Selective breeding enhances coral heat tolerance even over small spatial
 scales
 [https://doi.org/10.5061/dryad.7wm37pw3x](https://doi.org/10.5061/dryad.7wm37pw3x) ## Description of the data and file structure ### Description Physiological responses of coral adults from thermally distinct reefs Oyster Stacks (OS) and Pelican Point (PP) in the Ningaloo (Western Australia) and their selected larval offspring from reproductive crosses (intrapopulation: OSxOS and PPxPP; interpolation: OSxPP and PPxOS) of Acropora species (A. tenuis and A. millepora) under experimental heat stress with control at 27.1 oC and heat temperatures of 31.0 oC (adults) and 35.5 oC (larvae).  Thermal regimes and history of the reefs (OS) and (PP) were investigated a priori to coral collection and selective breeding to select potentially thermally distinct coral populations across Ningaloo.  ### Files and variables All data files are uploaded as "Data". All package codes and scripts are uploaded as "Software".  #### File: ningaloo_reef_crw_sst_1985-2022.nc **Description:** daily Sea Surface Temperature (SST) for Ningaloo from 1985 to 2022 (latest data available at the time of download).  ##### Variables * daily Sea Surface Temperature (daily SST) (degree Celsius) #### File: ningaloo_reef_cortadv6_ssta_freq_1985_2022.nc **Description:** SSTA Frequency for Ningaloo from 1985 to 2022 (latest data available at the time of download).  ##### Variables * Sea Surface Temperature Anomaly Frequency (SSTA Frequency) (degree Celsius) #### File: ningaloo_reef_cortadv6_tsa_dhw_1985_2022.nc **Description:** TSA in Degree-Heating-Weeks for Ningaloo from 1985 to 2022 (latest data available at the time of download).  ##### Variables * Thermal Stress Anomaly in Degree-Heating-Weeks (TSA DHW) (degree Celsius-Week) #### File: ningaloo_reef_imos_hinawari-8_L3C_sst_1_hour_2016-2022.nc **Description:** hourly Sea Surface Temperature (SST) for Ningaloo from 2016 to 2022 (latest data available at the time of download).  ##### Variables * hourly Sea Surface Temperature (hourly SST) (degree Celsius) #### File: RReady_Percentage_Larvae_Survival_Heat_Stress_HeatTolNing2023.csv **Description:** Heat stress response (i.e., survival) of the individual selected *A. tenuis* and *A. millepora* larvae from the initial timepoint to the final timepoint (~50% mortality) in the heat stress assay.  ##### Variables * Timepoint: Sequential time point of response measurements during the larval heat stress assay, numbered from 0 to 13 for *A. tenuis* larvae and 0 to 9 for *A. millepora* larvae. * Date: Date in the format mm/dd/yy for each timepoint of the larval heat stress assay * Year: Year for each timepoint of the larval heat stress assay–only 2023 * Time: Time in the format HH:MM for each timepoint * Treatment: Experimental treatment in the larval heat stress assay. *Ambient* (control) was maintained at 27.1 °C, and *Heat* (heat stress) was maintained at 35.5 °C * Temp: Water temperature for each treatment: 27.1 °C for *Ambient* and 35.5 °C for *Heat*. * Cone: Number of cone used in rearing individual selected larval families * Culture: Larval culture for a specific reproductive cross of eggs and sperm from unique spawning parental colonies of *A. tenuis* and *A. millepora*. Code legend: OT = *A. tenuis* colony from Oyster Stacks, PT: *A. tenuis* colony from Pelican Point, OM = *A. millepora* colony from Oyster Stacks,  PM = *A. millepora* colony from Pelican Point * Family: Number of family produced for each reproductive cross type: * Intrapopulation crosses: Oyster Stacks (OS) X Oyster Stacks (OS); Pelican Point (PP) X  Pelican Point (PP) * Interpopulation crosses: Oyster Stacks (OS) X Pelican Point (PP); Pelican Point (PP) X Oyster Stacks (OS)– with maternal colony listed first * ReefMom: Identification number of maternal colony used in reproductive cross to produce specific larval families. Same code legend as in "Culture" variable * Mom: Same as ReefMom * Dad:  Identification number of paternal colony used in reproductive cross to produce specific larval families. Same code legend as in "Culture" variable * Species: Represents species of larvae– *A.ten* = *A. tenuis* and *A.mil* = *A. millepora* * Boat.ID: Unique identification number assigned to the floating unit used in the heat stress assay, which contained netwell inserts holding individual replicates of larval families * Wells: Identification letter assigned to each well within an individual floating unit, representing a single replicate of a larval family * No.LarvaeInExpected * No.LarvaeInObserved: Total initial number of larval replicates for each unique family. Each netwell contained 20 larvae per family * Percent_Survival_atend: Percentage of larval survival at each timepoint, calculated as the number of live larvae divided by the total initial number of larvae (*n* = 20) in each netwell * CrossType: Type of reproductive cross, where *IndivCross* denotes that each cross was performed by selecting gametes from individual maternal and paternal colonies rather than as a bulk cross. * Lifestage: Developmental stage of coral used in the heat stress assay; only competent larvae were included   * Dataform: Data type, where *raw* indicates direct visual counts of larvae from observations without transformation or summarisation * Cumulative.hrs: Total elapsed hours since the start of the heat stress assay * Mom2: Origin of the maternal colony used in reproductive crosses: *PelMom* = maternal colony from Pelican Point; *OysMom* = maternal colony from Oyster Stacks * Dad2: Origin of the paternal colony used in reproductive crosses: *PelDad* = paternal colony from Pelican Point; *OysDad* = paternal colony from Oyster Stacks * Cross: Type of reproductive cross (intrapopulation or interpopulation) based on the origin of maternal and paternal colonies, using the codes from **Mom2** and **Dad2**  * Cross2: Type of reproductive cross (intrapopulation or interpopulation) based on the origin of maternal and paternal colonies, coded by source reefs (*OS* = Oyster Stacks; *PP* = Pelican Point) * Lineage.purity: Reproductive lineage category used in the selective breeding design: *purebred* (intrapopulation crosses) or *hybrid *(interpopulation crosses) #### File: RReady_KM_t0t9_Amil_Larvae_Mortality_Heat_Stress_HeatTolNin2023.csv **Description:** selected *A. millepora* larvae mortality from T initial to T final (~50% mortality), formatted Kaplan-Meier analysis.  ##### Variables * Same variables and descriptions as in RReady_Percentage_Larvae_Survival_Heat_Stress_HeatTolNing2023.csv * NoInd: Unique identifier assigned to each individual *A. millepora* larva counted within a netwell, across all floats and both treatments (Ambient and Heat). Values range sequentially from 0 to 20, corresponding to the 20 larvae from a single family per netwell  * Event: Mortality status for each individual *A. millepora* larva, recorded as a binary variable (0 = alive; 1 = dead) #### File: RReady_KM_t0t13_Aten_Larvae_Mortality_Heat_Stress_HeatTolNin2023.csv **Description:** selected *A. tenuis* larvae heat stress responses from T initial to T final (~50% mortality), formatted Kaplan-Meier analysis. ##### Variables * Same variables and descriptions as in RReady_Percentage_Larvae_Survival_Heat_Stress_HeatTolNing2023.csv * NoInd: Unique identifier assigned to each individual *A. tenuis* larva counted within a netwell, across all floats and both treatments (Ambient and Heat). Values range sequentially from 0 to 20, corresponding to the 20 larvae from a single family per netwell  * Event: Mortality status for each individual *A. tenuis* larva, recorded as a binary variable (0 = alive; 1 = dead) #### File: Adult_Heat_Stress_HeatTolNing2023_Curated.csv **Description:** *A. tenuis* and *A. millepora* adults heat stress responses from T initial to T final (~50% mortality). ##### Variables * Treatment: Experimental treatment in the adult heat stress assay. *Ambient* (control) was maintained at 27.1 °C, and *Heat* (heat stress) was maintained at 31.0 °C * Temp: Water temperature for each treatment: 27.1 °C for *Ambient* and 31.0 °C for *Heat* * Tank: Identifier for the tank used in the adult heat stress assay * Stick: Coral fragment plug holder containing 10 coral fragments, labelled from A to E. Each tank contained five sticks * Position: Position number of each coral fragment plug within a stick, labelled from 0 to 10  * Frag_tank_ID: Unique identifier for each coral fragment, derived from the combination of treatment, stick, and position * Genotype: Unique identifier for the source coral colony, coded as follows: *OT* = *Acropora tenuis* from Oyster Stacks; *PT* = *A. tenuis* from Pelican Point; *OM* = *Acropora millepora* from Oyster Stacks; *PM* = *A. millepora* from Pelican Point * Population: Reef source of coral colonies, coded as *OS* = Oyster Stacks; *PP* = Pelican Point * Species: Coral species of the colony (*Acropora tenuis* or *Acropora millepora*) * Date: Sampling date for each time point of the adult heat stress assay, in YYYY-MM-DD format * Timepoint: Sequential time point of response measurements during the adult heat stress assay, numbered from 0 to 6 * Survival: Survival status of each coral fragment, recorded as a proportion (1 = alive; 0 = dead) * Percent_Survival: Survival status of each coral fragment expressed as a percentage (100% = alive; 0% = dead) * FvFm: Effective photosynthetic yield (maximum quantum yield of photosystem II) of each coral fragment, expressed as a unitless value ranging from 0 to 1 * Bleaching_Score: Bleaching severity in each coral fragment, scored from 1 to 6, where lower scores indicate more severe bleaching * Tissue_Area: Total live tissue area of each coral fragment, measured in cm² * Necrosis_Area: Total area of tissue loss for each coral fragment, measured in cm² * Percent_Necrosis: Proportion of tissue loss for each coral fragment, expressed as a percentage of the total tissue area (100% = complete tissue loss; 0% = no tissue loss) #### File: RReady_KM_Aten_Adults_Heat_Stress_HeatTolNing2023.csv **Description:** *A. tenuis* adults heat stress responses from T initial to T final (~50% mortality) formatted for Kaplan-Meier (KM) analysis. ##### Variables * Same variables and descriptions as in Adult_Heat_Stress_HeatTolNing2023_Curated.csv * Mortality: Mortality event as 0 = alive or 1 = dead #### **File: RReady_KM_Amil_Adults_Heat_Stress_HeatTolNing2023.csv** **Description:** *A. millepora* adults heat stress responses from T initial to T final (~50% mortality) formatted for Kaplan-Meier (KM) analysis. ##### Variables * Same variables and descriptions as in Adult_Heat_Stress_HeatTolNing2023_Curated.csv * Mortality: Mortality event as 0 = alive or 1 = dead #### File: Parental_Colonies_Heat_Stress_Last_Timepoint_HeatTolNing2023.csv **Description:** *A. tenuis* and *A. millepora* parental colonies heat stress responses at T final (~50% mortality). ##### Variables * Same variables and descriptions as in Adult_Heat_Stress_HeatTolNing2023_Curated.csv but for the last timepoint of the adult heat stress assay only  #### File: DHW__Enhancement_Calculations_Larval_Heat_Stress_HeatTolNing2023.csv **Description:** Calculation of Degree-Heating-Weeks (DHW) enhancement for both *A. tenuis* (Aten) and *A. millepora* (Amil) based on experimental heat stress (temperature and duration), local Maximum Monthly Means at Oyster Stacks (OS) and Pelican Point) for present time and end-of-century based on a 1.4oC warming (RCP4.5). Using the NOAA Coral Reef Watch DHW formula. ##### Variables * Time of heat stress: Timepoint used in the calculation of the accumulated heat stress as Degree-Heating-Weeks (DHW) for selected larvae * MMM: Maximum Monthly Mean in degree Celsius * Temp (experimental): Temperature used in the heat treatment of the larval heat stress assay, which was 35.5oC * Hotspot Anomaly (Temp-MMM): Temperature anomaly based on the temperature differential between the temperature in the larval heat stress assay (Temp (experimental)) and the Maximum Monthly Mean (MMM) calculated for each source reef * Hours (experiment): Total number of accumulated hours during the larval heat stress assay * Weeks (experiment): Total number of weeks accumulated during the larval heat stress assay converted from the total number of hours * DHW: Degree-Heating-Weeks in degree Celsius-Week ### Code/software Free open software R Studio with R version 4.2.2 (2022-10-31) was used to open, visualize and analyze all datasets.  #### Package codes To run and analyze the files of temperature metrics, the following R packages should be loaded from the script `sst_packages_final:`  `library(ncdf4)` `library(RNetCDF)` `library(ncdf.tools)` `library(xts)` `library(lubridate)` `library(zoo)` `library(cowplot)` `library(MoMAColors)` `library(ggplot2)` `library(ggpubr)` `library(raster)` `library(dplyr)` `library(tidyr)` `library(tidyverse)` `library(abind)` `library(sf)` `library(gridExtra)` `library(stats)` `library(mgcv)` `library(e1071)` `library(effsize)` `library(broom)` `library(car)` To run and analyze the files of both adults and larvae heat stress responses, the following R packages should be loaded from the script `heat_stress_adults_&_larvae_packages`:  `library(plyr)` `library(dplyr)` `library(tidyr)` `library(ggplot2)` `library(ggpubr)` `library(ggsignif)` `library(RColorBrewer)` `library(ggsci)` `library(scales)` `library(massageR)` `library(gplots)` `library(tidyverse)` `library(gridExtra)` `library(survival)` `library(survminer)` `library(bshazard)` `library(Rmisc)` `library(readxl)` `library(rstatix)` `library(coin)` `library(sjPlot)` `library(carData)` `library(car)` `library(nlme)` `library(lme4)` `library(pscl)` `library(MASS)` `library(multcomp)` `library(emmeans)` `library(sandwich)` `library(lmtest)` `library(DHARMa)` `library(patchwork)` `library(TMB)` `library(glmmTMB)` `library(betareg)` `library(lubridate)` `library(broom)` `library(forcats)` #### Scripts List of scripts provided in the submission for data exploration, visualization and analysis in R Studio: For thermal metrics of Oyster Stacks (OS) and Pelican Point (PP) reefs across the two time periods (historical 1985-2010 and post-MHW 2010-2022):  * **Monthly and annual Sea Surface Temperature (SST)**: `crw_sst_means_stdevs_ningaloo_final.R` * **Sea Surface Temperature Anomaly (SSTA) Frequency**: `ssta_freq_stdev_ningaloo_final.R` * **Thermal Stress Anomaly in Degree Heating Weeks (TSA DHW)**: `tsa_dhw_stdev_ningaloo_final.R` * **Sea Surface Temperature - Daily Temperature Range (SST DTR)**: `sst_dtr_ningaloo_final.R` For *A. tenuis* and *A. millepora* adult heat stress assay: * Endpoint heat stress responses (survival, necrosis, bleaching, fvfm) : `Boxplots_traits_adults_final.R` * Heat stress responses analysis for *A. millepora*: `Models_amil_adults_heat_stress_final.R` - Heat stress responses analysis for *A. tenuis*: `Models_ten_adults_heat_stress_final.R` * Means of heat stress responses for *A. tenuis* and *A. millepora* adults (all from both populations): `means_traits_adults_heat_stress.R` - Means of heat stress responses for *A. tenuis* and *A. millepora* parental colonies only: `means_traits_parents_heat_stress.R` * Kaplan-Meier (KM) survival analysis for *A. millepora*:` KM_amil_adult_survival_heat_stress_final.R` - Kaplan-Meier (KM) survival analysis for *A. tenuis*:` KM_aten_adult_survival_heat_stress_final.R` For *A. tenuis* and *A. millepora*  selected larvae heat stress assay: * Kaplan-Meier (KM)survival analysis for *A. millepora*: `KM_amil_larvae_survival_heat_stress_final.R` - Kaplan-Meier (KM) survival analysis for *A. tenuis*: `KM_aten_larvae_survival_heat_stress_final.R` - Endpoint heat stress survival by family and cross type of selected larvae of *A. tenuis* and *A. millepora*: `Survival_larval_by_family&cross.R` ### Access information Other publicly accessible locations of the data: * To be available on a GitHub repository once published.  Data was derived from the following sources: * NOAA CRW 5 km and NOAA CoRTAD 4 km derived via a THREDDS (Thematic Real-time Environmental Distributed Data Services) Data Server (TDS) of NOAA NCEI.  * IMOS Hinawari-8 2 km derived from IMOS AODN online data catalog.