Parental coral colonies of A. tenuis and A. loripes were collected from Trunk Reef on the central Great Barrier Reef in November 2015. During spawning, four offspring groups (i.e., reciprocal F1 hybrids and two parental purebreds: TT (purebred A. tenuis), TL (hybrid), LT (hybrid) and LL (purebred A. loripes), were recruited and settled onto ceramic plugs. Detailed crossing protocol and experimental design is described in Chan et al. (2018). Coral recruits were reared under treatment conditions in filtered seawater for seven months at the National Sea Simulator of the Australian Institute of Marine Science. Treatment conditions included exposure to ambient or elevated temperature and pCO2 conditions: ambient conditions (27ºC and 415 ppm pCO2) elevated conditions (ambient +1 °C and 685 ppm pCO2) RNA-sequencing was conducted and the analysis showed that gene expression of the hybrid Acropora also showed clear maternal effects. Further details are presented in the paper Chan, WY, Chung, J, Peplow, LM, Hoffmann, AA, van Oppen, MJH. Maternal effects in gene expression of interspecific coral hybrids. Mol Ecol. 2021; 30: 517– 527. https://doi.org/10.1111/mec.15727

Wild coral colonies of Acropora tenuis were collected throughout the Great Barrier Reef and transferred to the Australian Sea Simulater (SeaSim). Corals were spawned, and produced purebred and hybris crosses, see Quigley & van Oppen (2022) and Dixon & Kenkel (2019) for full details of spawning and reproductive crossing. Larvae produced from these crosses were sampled for gene expression and assayed using RNAseq before being exposed to control and heat stress for 36 hours (27 and 35.5 °C) in replicates of n=6 (“post” exposure samples). Separate cohorts of each larval cross not used in the heat trials were then induced to settle and exposed to four symbiont treatments. These replicates were sampled for RNAseq for each of the crosses prior to the heat stress at time 0 and 56 hours at 27°C and 35.5°C treatments. For survival measurements, individual larvae were counted within net-wells in replicate plates within each temperature treatment. Each larval survival measurement represents a discrete sample measurement. The unit of measure is the number of individual replicate wells containing larvae. Juvenile replicates RNAseq samples were taken in each of the crosses after 58 days at 27 and 32°C. Survival measurements represent individual juvenile survival. Each represents a discrete sample measurement. The unit of measure is the number of individual replicate juveniles per replicate well, per replicate plate, per replicate tank for each temperature and symbiont treatment. Larval survival was counted from 0 to 56 hours at 27°C and 35.5°C. Juvenile survival was counted at 0 and after 58 days at 27 and 32°C treatments. Larvae were assayed for RNAseq at 0 and 56 hours, and juveniles only at 58 days. Experimental metadata of detailed replicates for larval treatments are found on the github repository in file J19188meta.csv. For“pre”, and “post-ambient” there were 33 larval replicates. For “post-hot” there were 30 replicates. Each replicate represented 10 pooled larvae. Each of the 11 crosses was replicated 3 times within each of those 3 treatment groups. There was a total of 96 larval samples. Experimental metadata for juvenile data is found on the github repository in file J19234meta.csv. Of the juvenile samples, 119 werein ambient conditions with 27 in the heat treatment. Each of the 10 crosses was represented in the juvenile dataset 12-18 times. Thesymbiont treatments had 29 samples in C1, 38 samples in D1, 43 samples in SED, and 36 in SS1. There was a total of 146 juvenile samples. Derived statistics presented are defined as independent observations of n= independent larval or juvenile survival based on the number

Fertile hybrids can enhance the adaptive capacity and resilience of species under stress by increasing genetic diversity within populations, masking the effects of deleterious recessive alleles, and facilitating the introgression of beneficial genetic variants into parental species. However, many hybrids are infertile. We compared the fertility of aquarium-reared F1 hybrid and purebred corals of the species Acropora loripes and Acropora kenti and examined the viability of early life stages of second-generation (F2) hybrid and back-crossed planula larvae and recruits. The F1 hybrids spawned viable gametes and the F2 hybrid and back-crossed embryos developed into planula larvae and settled to become sessile coral recruits. The F1 hybrids had greater reproductive fitness than the F1 A. loripes purebred stock in an aquarium environment based on their probability of spawning and their fertilization success in crosses using their gametes. Interspecific coral hybrids can therefore be fertile and have high reproductive fitness, which could benefit the persistence of threatened coral reefs.

Interspecific hybridisation increases genetic diversity and has played a significant role in the evolution of corals in the genus Acropora. In vitro fertilisation can be used to increase the frequency of hybridisation among corals, potentially enhancing their ability to adapt to climate change. Here, we assessed the field performance of hybrids derived from the highly cross-fertile coral species Acropora sarmentosa and Acropora florida from the Great Barrier Reef. Following outplanting to an inshore reef environment, the 10-month survivorship of the hybrid offspring groups was intermediate between that of the purebred groups, although not all pairwise comparisons were statistically significant. The A. florida purebreds, which had the lowest survivorship, were significantly larger at 10 months post-deployment compared to the other three groups. The four offspring groups harboured the same intracellular photosymbiont communities (Symbiodiniaceae), indicating that observed performance differences were due to the coral host and not photosymbiont communities. The limited differences in the performance of the groups and the lack of outbreeding depression of the F1 hybrids in the field suggest that interspecific hybridisation may be a useful method to boost the genetic diversity, and as such increase the adaptive capacity, of coral stock for restoration of degraded and potentially genetically eroded populations.

Symbiodinium communities in the brooding coral Seriatopora hystrix were examined to determine the extent of hereditary and environmental influence on the structure of Symbiodinium communities. Symbiont communities within 60 larvae and their parents (9 maternal and 45 paternal colonies) were genotyped using high-throughput sequencing of the ITS2 locus.

Acropora cervicornis, A. palmata and Orbicella faveolata are important reef-building coral species in the Florida Reef Tract (FRT). These species have experienced alarming declines throughout the FRT, resulting in an increased risk of inbreeding depression and susceptibility to decreased fitness in surviving colonies. Acropora cervicornis, A. palmata and O. faveolata are broadcast spawners, introducing genetic diversity through sexual recombination of gametes during annual spawning events. Successful reproduction during this time is critical for curbing the deleterious effects of inbreeding depression, and in successfully restoring wild colonies to self-sustaining levels of genetic diversity. A critical step in the reproductive cycle of these species is the success of gamete fertilization following mass spawning events. Several abiotic causes of gametic incompatibilities have been reliably observed in these species, and incompatibility between certain genotypes has been shown to occur. This dataset represents the collection of gametes from three coral species following nine spawning events in the Florida Keys during two spawning years (2019 and 2022), reciprocal fertilization trials with gametes from each parent and determined fertilization success for each cross. Additionally, tissue fragments were collected from each A. cervicornis parent, DNA was isolated from the tissue and single nucleotide polymorphism analyses were performed using the Axiom Coral-Algae Genotyping array (Axiom AcropSNP, ThermoFisher Scientific). This data package contains images of coral eggs post fertilization trial and the results in spreadsheet format. The raw A. cervicornis single nucleotide polymorphism (SNP) data are also provided.

To evaluate the effects of El Nino driven mass thermal stress on the coral Monitpora digitata during spawning in a severe bleaching year (2016). 32 colonies were collected, from a minimum of 5 - 10 metres apart laterally along the shore. Spawning occurred on 23rd April 2015, where egg-sperm bundles were collected from spawning colonies, total of 9. 27 of these colonies were re-collected from Hazard Bay in April 2016 and 5 remaining colonies were presumed dead. Colony colouration was assessed using the CoralWatch Color Chart, with photographs alongside each colony at the time of collection. Spawning occurred on 24th April 2016, and a total of 4 were spawning colonies. To determine the effects of thermal stress and the presence of bleaching in 2016, the health of coral colonies were measured using methods of effective quantum yield of photosystem II (YII), colony coloration, and Symbiodiniaceae cell density. YII was measured using Pulse Amplitude Modulated fluorometry (PAM) with a fibre optic cable (diving-PAM, Waltz). Samples from all spawning adults and 10 – 12 eggs from each colony were genotyped in both 2015 and 2016 through ITS2 amplicon sequencing. Analysis of community composition was achieved through sequence variations, evidence of shuffling of Symbiodiniaceae communities and differences in Symbiont densities and photochemical efficiencies.

This study whether corals from the warmer reef produced more thermally tolerant hybrid and purebred offspring compared with crosses produced with colonies sourced from the cooler reef and whether different symbiont taxa affect heat tolerance. Juveniles were infected with Symbiodinium tridacnidorum, Cladocopium goreaui and Durusdinium trenchii and survival, bleaching and growth were assessed at 27.5°C and 31°C. The experiment focused on familial crosses produced from (n=3) parents from a warm far northern reef (WW1, WW2, WW3), one cross with a warm dam and cool sire (WC) and one cross with a cool dam and warm sire (CW). Larvae from each cross were allowed to settle, and grown on plugs for 11 days. Juveniles were exposed to one of three treatments of the following Symbiodiniaceae taxa cultured at the Australian Institute of Marine Science Algal Culture Facility: S. tridacnidorum (monoclonal SCF022.01), C. goreaui (monoclonal SCF055-01.10) and D. trenchii (heterogeneous SCF082) as described in Quigley et al. (2014) All inoculated juveniles were subsequently kept at 27.5°C for 8 days and symbiosis establishment was visually confirmed over this period under a microscope. Plugs were then randomly divided across treatment tanks, and half from each symbiosis-establishment treatment were placed into 31°C treatment tanks without ramping, totalling six tanks (three replicate tanks at 27.5°C and three replicate tanks at 31°C). Juvenile survival, bleaching and growth were assessed through image analysis, starting on the first day of exposure to 31°C, with five time points measured and analysed at 1, 9, 35, 49 and 70 days of heat exposure. Juveniles were scored as highly pigmented (3=D6), pale (2=D4), bleached (1=D1, translucent tissue), or dead (0, missing or bare skeleton with or without algal or cyanobacterial overgrowth) Statistical analyses completed in R using generalisezd linear models and percent change in the bleaching score and juvenile area were calculated for each individual juvenile across host genetic background and symbiont type. See Quigley et al (2020) for full details.

An 18-month reciprocal field transplant experiment was undertaken to examine the environmental and genetic drivers behind variation in survival, weight gain, heat tolerance and algal symbiont community between the reef flat and slope habitats. Pocillopora damicornis colonies from Heron Island were used in a two-part experiment of a replicated RTE across depth habitats and a common garden stress test. Three vital traits were measured between March 2012 – August 2013., and then the relative heat tolerance was measured by exposing the surviving colonies to 14 days of ex situ experimental heat stress. At each site and habitat, 23 – 26 colonies were collected (total n = 97) and fragmented into two halves. One half of each colony was places onto experimental rack in its habitat of origin and the other haps was transplanted to the reciprocal habitat within each site. 2 x 2 m wire mesh racks were installed approximately 0.5m above the substrate and fragmented coral colonies were attached across the rack with cable ties in a haphazard manner. This resulted in four treatment groups replicated at two sites: flat to flat (FF), flat to slope (FS), slope to flat (SF), and slope to slope (SS). Partial colony mortality and weight gain were measured in the field four times between March 2021 and August 2013. A number of colonies were sampled for Symbiodiniaceae community in coral tissue per site and treatment group at two time points in April 2012 and March 2013. At the end of the field transplant experiment on 17 August 2013, the remaining live colonies were transported to the Australian Institute of Marine Science in Townsville, and kept in outdoor 1000L tanks for 10 days. They were then further fragmented into single branches and acclimatized in indoor 30L flow-through tanks at 24°C. Treatment temperatures for the heat stress exposure included 24°C, 29°C, 30°C and 31°C. Between 3 and 20 replicate fragments per colony were exposed each temperature level, for a total of 14 days heat stress. Heat tolerance was quantified by proxy of the maximum quantum yield (Fv/Fm), measured with Pulse-Amplitude Modulation (PAM) fluorometry. Analyses were conducted of Symbiodiniaceae community composition by source and transplant habitats (flat and slope) and physiological traits, percent partial mortality and percent cumulative weight gain. Heat stress analysis was also conducted among different temperatures and contrasts of treatment groups. See published papers linked below for further details.

The distribution of genetic variation of 7 microsatellite DNA markers in the mass-spawning coral Acropora tenuis was measured to infer patterns of connectivity among reef systems in the offshore (Scott Reef and Rowley Shoals) and coastal (Dampier Archipelago and Ningaloo Reef) zones of northwest Australia.Samples from 1156 colonies of Acropora tenuis were collected from 6 or 7 sites (more than 40 colonies were collected from most sites) at each of the Scott Reef, Rowley Shoals, Ningaloo Reef and the Dampier Archipelago systems.To minimize multiple collections of the same genet that may have been produced through asexual fragmentation or propagation (ramets), only a colony that was physically distinct and more than 1.5 m from other colonies was sampled. Note this provided an unbiased underestimate of the real contribution of asexual reproduction. Clonality was measured by calculating the proportion of unique multilocus genotypes as (Ng:N) at each site: of the 1156 samples collected, 1061 had unique multilocus genotypes.To explore the historical genetic connections among sites and systems, the amount of genetic variation were analysed within and among sites with respect to different alleles (FST), and on the sum of squared size differences of the alleles, assuming a stepwise model of mutation (RST).To further quantify the relationships among sites, 3 genetic distance measures between pairs of sites were calculated: DLR, which compares the likelihoods of complete multilocus genotypes in two populations; DS, Nei's standard genetic distance; and pairwise FST.Genetic diversity measures were calculated with FSTAT v2.9.3 as an unbiased estimate of gene diversity (HSK) and allelic richness (RS) per locus and site. The loci names use a prefix for the species followed by 2 or 5 according to the repeat motif type (di- or pentamer), followed by a number: Amil2-006, Amil2-010, Amil2-011, Amil2-012, Amil2-018, Amil2-022, Amil5-028. To assess genetic structure and diversity using 7 DNA microsatellite loci of the mass-spawning hard coral, Acropora tenuis, from a series of isolated and discontinuous coastal and offshore reef systems in northwest Australia.To test whether genetic and genotypic (clonal) diversities vary between the high-latitude, offshore reefs and the low latitude, coastal reefs.To gain further insight into degree of isolation, effective population size and the importance of asexual versus sexual reproduction.