DOI: 10.5061/dryad.x3ffbg7t8
title: Data from: Reproductive resilience: Pathways to gametogenic success in Montipora capitata after bleaching

description: Thermal bleaching, or the loss of symbiotic algae that provide most
 energetic resources for the coral host, is an increasing threat to reefs
 worldwide and is projected to worsen with climate change. While this
 threat to coral persistence is well recognized, the impact on the
 essential process of reproduction in corals that survive bleaching is not
 well resolved despite being central to coral resilience. Montipora
 capitata can survive thermal bleaching while completing a full gametogenic
 cycle, offering an ideal system to study gametogenic resilience and
 associated physiological tradeoffs. We experimentally bleached fragments
 of M. capitata colonies and followed their gametogenic cycle and
 physiological responses for 10 months at six time points. All bleached
 colonies produced gametes at the same time as controls, suggesting that
 reproductive processes were energetically prioritized. However, proteomic
 analysis across the gametogenic cycle revealed tradeoffs and delays in
 activating key physiological processes earlier in gametogenesis in areas
 such as skeletal growth and reproductive hormone synthesis. Tradeoffs
 during the gametogenic cycle, likely a direct response to thermal
 bleaching, resulted in smaller oocytes from bleached colonies than
 controls, potentially indicating decreased transfer of parental resources
 to the gametes. While gametogenesis is likely to continue in this species,
 it remains to be seen how the viability and success of future offspring
 may be impacted by continued future bleaching events.
description: Seventy-four <em>M. capitata</em> coral
 (approximately 30 cm in diameter) were collected from patch reefs located
 in Kāneʻohe Bay, Oʻahu, Hawaiʻi around the Hawaiʻi Institute of Marine
 Biology (HIMB, 21.428°N, 157.792°W) in August 2017. Each coral was divided
 in half, with one half assigned to the control group and the other to the
 thermal bleaching group. Samples were collected pre-bleaching and at 5
 time points post-bleaching and through spawning. Histology was perfomed on
 the last two time points during the spawning season (June and July). Using
 histology, data were collected on oocyte and spermatocyte stage, oocyte
 Feret diameter, and fecundity. Chlorophyll, symbiont counts, symbiont
 clade (using qPCR), and total lipids were also measured. Protein was
 extracted from each coral sample, digested with trypsin, and analyzed on a
 Q-Exactive-HF mass spectrometer using data dependent acquisition. Raw mass
 spectra were searched against a species-specific predicted proteome using
 Comet and Peptide and ProteinProphet, followed by Abacus with an FDR
 cut-off of 0.01.
description: # Data from: Reproductive resilience: Pathways to gametogenic success in
 Montipora capitata after bleaching
 [https://doi.org/10.5061/dryad.x3ffbg7t8](https://doi.org/10.5061/dryad.x3ffbg7t8) This dataset contains data files and R code necessary to reproduce the figures and analysis presented in the accompanying manuscript published in Scientific Reports, "Reproductive resilience: Pathways to gametogenic success in *Montipora capitata* after bleaching". This includes figures summarizing the histological data and analysis with linear models; figures and linear models of total lipid, chlorophyll, and symbiont data; PLS-DA (partial least squares discriminant analysis) of the proteomics data; hierarchical cluster analysis of the proteomics data; and symbiont qPCR analysis. ## Description of the data and file structure **Histology:** montipora time series oocytes.csv * *Sample:* Unique coral sample identifier * *Treatment*: whether or not the coral fragment underwent experimental bleaching; Bleached or Non-bleached * *Time*: Time point at which sample was collected; T5 = June * *Stage*: Oocyte stage of development; I, II, III or IV * *area*: Oocyte area, numeric * *feret*: Oocyte Feret diameter, a measure of oocyte size * *feret_bin* * *NewStage:* Numeric value (1-4) for oocyte stage montipora time series sperm.csv * *Sample:* Unique coral sample identifier * *Stage I*,* Stage II, Stage III, Stage IV:* The number of histological observations of coral sperm at each stage of development * *Total Observations*: Total observations made of sperm The R code file, including all necessary R packages, is called "mcap* *time series histo.R". **Physiology:** Mcap time series chlorophyll.csv * *Colony*: Coral genet identifier * *Status*: Bleaching status; na for pre-experimental bleaching time point, B = if the coral was bleached and NB = if the coral was in the non-bleached control group * *Time*: Sampling time point (0-6) * *Date:* Calendar date of each sampling time point * *Chl a ug/g*: chlorophyll a measured in micrograms per gram coral tissue * *Chl c2 ug/g*: chlorophyll c2 measured in micrograms per gram coral tissue * *Tolerance*: Indicates whether or not the coral genet survived bleaching (resilient, "R") or died (susceptible, "S") Mcap time series symb counts.csv * *Colony No.*: Coral genet identifier * *Bleaching Status*: na for pre-experimental bleaching time point, B = if the coral was bleached and NB = if the coral was in the non-bleached control group * *Time: *Sampling time point (0-6) * *Tolerance*: Indicates whether or not the coral genet survived bleaching (resilient, "R") or died (susceptible, "S") * *Symbionts per dry tissue mass (g):* Number of symbionts per gram of coral dry tissue * Unnamed column: Calendar date of each sampling time point egg size 2009.csv * *Date*: Date coral collected * *Avg egg size*: Average Egg Feret Diameter * *Egg stdev*: Standard deviation of egg size * *Egg stderr*: Standard error of egg size lipid analysis.csv * *Baggie ID*: Unique coral identifier * *ID*: Coral genet identifier * *Status*: Bleaching status; na = pre-experimental bleaching timepoint, B = experimentally bleached, NB = non-bleached control * *Tolerance*: Indicates whether or not the coral genet survived bleaching ("resilient", R), or died (susceptible, "S") * *Lipid/Biomass (g/gdw)*: Grams of lipid per gram dry weight coral tissue * *Tolerance.Time*: Combined variable for coral bleaching tolerance and sampling time point * *Date*: Calendar date for sample collection The R file for the figure is called "physiology R script". The R file for the linear models is called "lmer". **Symbiont clade qPCR**: final_datav3_colonies.csv * *well_name*: Label for qPCR well, includes time point and coral genet identifier * *c_mean*: Mean abundance of symbiont clade C * *c_sd*: Standard deviation of symbiont clade C * *d_mean*: Mean abundance of symbiont clade D * *d_sd*: Standard deviation of symbiont clade D * *presence*: Which clades are present in each sample; C = C only, D = D only, CD = both * *cd_ratio*: C abundance/D abundance * *prop_d*: Proportion of D clade based on mean abundance * *prop_c*: Proportion of C clade based on mean abundance * *abundance*: Indicates the dominant clade; if C dominates = C&gt;D, if D dominates = D&gt;C * *sd**_warning* * *ct_warning* * *rep* * *C*: Percent C clade * *D:* Percent D clade The R file is "symbiont_clades_mcap_time_series_adults". **PLS-DA**: NSAF outliers removed.csv * Column 1: Mass spectrometry sample names * Columns 2 - 4345: Proteins inferred in the mass spectrometry workflow. Values in the cells represent protein abundance for each sample measured. annotation_Shumaker2019.txt * *gene_id*: Protein ID from the fasta database used for protein inference * *description*: NCBI accession number from BLAST annotation of the fasta * *length*: Protein length * *eValue*: e-value statistic for BLAST * *bitscore:* BLAST statistic * *simMean*: BLAST statistic * *UniprotKB_entry*: Uniprot database annotation of protein sequence * *status*: Review status of Uniprot protein annotation * *protein_names*: Name of Uniprot protein * *gene_names*: Uniprot protein gene name * *organism*: Organism in which Uniprot protein was sequenced * *ko*: KEGG Ortholog for the annotation * *GO_IDs*: Gene Ontology ID association with annotation * *GO_terms*: Gene Ontology term that described the GO ID Parallel workflows for bleached and non-bleached corals were followed with the separate R files "PLSDA bleached" and "PLSDA non-bleached". The source code for the R package biostats is provided to complete the analysis. **Hierarchical clustering**: Coral Time Series Shumaker NSAF.csv * Column 1: Protein name from fasta used for protein inference * Columns 2 - 79: Sample IDs for each coral sample analyzed in the format GenetID, Bleaching status, Time point, sample identifier, e.g., 66BT6_74 is from genet 66, bleached, time point 6, sample 74 The two files "cluster assignments NB/B hierarchical 0.6.csv" are generated in the workflow and provided for ease of completion. The R script is called "hierarchical cluster R script".