Simualted Data for ILS Null Slow Rate

This file contains the simulated data used to create the null distributions for the test of incomplete lineage sorting in Callyspongia vaginalis based on the slow substitution rat

ENA_accession_numbers_and_sequences

ENA_accession_numbers_and_sequence

Simulated Data For SumStat Test

This file contains the data simulated to test the performance of different summary statistics to detect incomplete lineage sorting. The name of each file indicates the age of the population divergence under which the data were simulated

Macrophage_expressed_protein

DNA sequences from Callyspongia vaginalis for the Macrophage expressed protein gene (partial coding sequence

Scripts_null_distributions

This file contains the ms and seqgen commands used to simulate the data used to create the null distributions in the hypothesis testing for incomplete lineage sorting in Callyspongia vaginali

Filamin

DNA sequences from Callyspongia vaginalis for the Filamin gene (partial coding sequence

Simualted Data for ILS Null Fast Rate

This file contains the simulated data used to create the null distributions for the test of incomplete lineage sorting in Callyspongia vaginalis based on the fast substitution rat

Elongation_factor1a

DNA sequences from Callyspongia vaginalis for the Elongation factor 1 alpha gene (partial coding sequence

Cathespsin

DNA sequences from Callyspongia vaginalis for the Cathepsin gene (partial coding sequence

Table_3_Host and Symbionts in Pocillopora damicornis Larvae Display Different Transcriptomic Responses to Ocean Acidification and Warming.DOCX

<p>As global ocean change progresses, reef-building corals and their early life history stages will rely on physiological plasticity to tolerate new environmental conditions. Larvae from brooding coral species contain algal symbionts upon release, which assist with the energy requirements of dispersal and metamorphosis. Global ocean change threatens the success of larval dispersal and settlement by challenging the performance of the larvae and of the symbiosis. In this study, larvae of the reef-building coral Pocillopora damicornis were exposed to elevated pCO₂ and temperature to examine the performance of the coral and its symbionts in situ and better understand the mechanisms of physiological plasticity and stress tolerance in response to multiple stressors. We generated a de novo holobiont transcriptome containing coral host and algal symbiont transcripts and bioinformatically filtered the assembly into host and symbiont components for downstream analyses. Seventeen coral genes were differentially expressed in response to the combined effects of pCO₂ and temperature. In the symbiont, 89 genes were differentially expressed in response to pCO₂. Our results indicate that many of the whole-organism (holobiont) responses previously observed for P. damicornis larvae in scenarios of ocean acidification and warming may reflect the physiological capacity of larvae to cope with the environmental changes without expressing additional protective mechanisms. At the holobiont level, the results suggest that the responses of symbionts to future ocean conditions could play a large role in shaping success of coral larval stages.</p