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

Fourteen colonies of A. tenuis were collected from Geoffrey Bay, Magnetic Island and transported to the National Sea Simulator Facility (SeaSim) at the Australian Institute of Marine Sciences (AIMS). Corals were maintained in outside aquaria prior to the spawning event Once larvae were competent to settle (7 days postspawning) preconditioned terracotta tiles crustose coralline algae (CCA) were introduced to induce settlement. Larvae were left to settle for 11 days. Settlement on each tile was assessed visually, and tiles containing juveniles were strung onto stainless steel rods in groups of 15 separated by PVC spacers. Nineteen days postspawning, 240 tiles, each with 40–200 juveniles, were transported to Magnetic Island and deployed at two sites at Magnetic Island (Geoffrey Bay and Nelly Bay) respectively, at a depth of approximately 6. Fluorescent microscopy was used to confirm the absence of Symbiodiniaceae cells prior to field deployment. Juveniles were sampled from tiles on the 19th of each month from 8:30 to 10:30 a.m. where conditions allowed, where between 6 and 17 juveniles were photographed at each time point. As juveniles began to present more complex branching patterns, 3D modelling was then employed to capture the geometries and estimate surface area. Surface area measurements were matched with Symbiodiniaceae cell counts and DNA extractions for each juvenile. The age of juveniles at each sampling time point was as follows: T1 – 40 days T2 – 71 days T3 – 11 days T4 – 129 days T5 – 167 days T6 – 194 days T7 – 316 days T8 – 380 days See Quigley et al (2020) for full details.

Data on the variation of microsatellite markers and changes in coral cover at 6 sites at Scott Reef were used to identify:1. At which sites were Seriatopora hystrix worst affected by bleaching.2. The scale of genetic subdivision of S. hystrix at Scott Reef 5 years after the bleaching event, and to what extent had the majority of larvae dispersed (metres or tens of kilometres).3. Whether new recruits at the most severely bleached sites were produced locally (from a few remaining colonies), from other sites on the same reef, or from other reefs within the Scott Reef system.All sites consisted of 5 permanent 50 m transects on the reef slope at about 9 m depth. Transects were filmed 6 months before (October 1997), 6 months after (October 1998), and approximately 5 years after (November 2003) a bleaching event which occurred in February 1998. Percentage cover (estimated using a point intercept method) was calculated from the mean percent cover over the 5 transects at each site for each year.In January 2004, 287 samples from individual colonies of S. hystrix were collected from 6 sites within the Scott system: south Scott (SL1, SL2 and SS1), north Scott (SL4), Sandy Islet Reef (SL5), and Seringapatam Reef (SS3). At each site, the exact location of each sampled colony along a permanent 300 m transect was recorded, along with the global positioning system coordinates at the beginning of each transect. Between 45 and 50 colonies were sampled at regular intervals along each transect.Genotyping of the 287 individuals was carried out. Because only two pairs of individuals shared the same diploid multilocus genotype, one individual from each of these pairs was removed from subsequent analyses so that each unique genotype was represented only once.Characteristics of the 9 Seriatopora hystrix microsatellite markers recorded were: the number of unique multilocus genotypes (N), the number of alleles (A), the proportion of observed (HO) and expected (HE) heterozygotes per locus and site, and the FIS calculated for each locus and each site (FIS All). Loci: Sh2-002, Sh2-006, Sh4-001, Sh4-010, Sh3-003, Sh3-004, Sh3-007, Sh3-008, Sh3-009, Sh4-001, Sh4-010. Allelic frequencies, allelic patterns and expected heterozygosities under Hardy-Weinberg equilibrium, and the number of private alleles were calculated in Genalex v6.Tests for Hardy-Weinberg and linkage disequilibrium were conducted using FSTATv2.9.3a spatial autocorrelation analysis, applied within each site. To explore the fine-scale processes influencing the local genetic structure and assess present day migration patterns over larger scales for S. hystrix at the Scott Reef system using high resolution genetic markers in combination with a detailed sampling design.To explore the influence of larval dispersal and adult abundances on rates of recruitment and recovery of this species following a catastrophic disturbance (bleaching) in an isolated system.

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.

Genetic variation was studied at 7 polymorphic allozyme loci in 15 Holothuria nobilis (now referred to as H. whitmaei) populations on the Great Barrier Reef. The 7 polymorphic enzyme loci surveyed using allozyme electrophoresis were: FL-EST, GPI, HK, MDH, MPI, PGM, TPI. Full details of staining and electrophoresis methods are given in:Ballment E, Uthicke S, Peplow L, Benzie JAH (1997) Techniques for enzyme electrophoretic analysis of the holothurians Holothuria atra and Stichopus chloronotus (Holothuroidea: Aspidochirotida). Aust Inst Mar Sci (AIMS) Tech Rep Ser 27:1-47Basic analyses of genetic variability were carried out using programs in the BIOSYS-1. F-statistics, cluster analyses and tests of conformation to Hardy-Weinberg expectations were performed using the TFPGA package. To infer the level of dispersal among populations of Holothuria nobilis separated by up to 1300 km along the Great Barrier Reef by investigating gene flow.To test whether asexual reproduction is a feature of this species. Reef locations: 13-050, 21-149, 21-151, Big Broadhurst, Davie, Davies Reef, East Cay, Hicks, Little Broadhurst, Michaelmas, Opal, Ribbon No.10, Stucco, Turner, White Tip.

To determine the impacts of future climate projections on the establishment of symbionts in juvenile corals, ITS2 amplicon sequencing of single coral juveniles was applied to Goniastrea retiformis and Acropora millepora before and after exposure to three climate conditions of varying temperature and pCO2 levels (current and RCP8.5 in 2050 and 2100). varying levels of temperature and pCO2: 2100 (+2°C offset, pCO2 940 ± 60ppm) 2050 (+1°C offset, pCO2 685 ± 60ppm) present day levels (28.5°C, pCO2 400 ± 60ppm) The dynamics of symbiont community changes (prevalence, relative abundance, and diversity) were assessed under exposure to these multiple climate treatments. G. retiformis was further assessed over time (0, 10 days and 4 weeks) and A. millepora further assessed at the final timepoint. DNA extraction and sequencing - Genomic DNA was extracted from G. retiformis and A. millepora samples across three sampling times (T0, T1 and T2), and treatments (ambient, 2050, 2100) with a total of 135 individual juvenile samples were successfully sequenced (27 samples belonged to A. millepora, and 110 belonged to G. retiformis ).

Population genetic structure was studied in one nearshore (Great Palm Island) and two offshore (Rib Reef and Reef 18-026) populations of Stichopus chloronotus on the Great Barrier Reef. Two stations approximately 500m were sampled on each reef at depths between 1 and 2 m. At each station, 30-40 individuals were sampled within a radius of 30m, in early November 1996. The sampling time in November was chosen to increase the likelihood of finding mature gonads in the sampled animals.Genetic variation at 5 polymorphic loci was examined using allozyme electrophoresis. The polymorphic enzymes examined were: hexokinase (E.C. 2.7.1.1; HK), mannose- 6-phosphate isomerase (E.C. 5.3.1.8; MPI), phosphoglucomutase (E.C. 5.4.2.2; PGM), triose-phosphate isomerase (E.C. 5.3.1.1; ¹PI) and peptidase using valylleucine as substrate (E.C. 3.4.11/13; Estimates of the level of asexual reproduction were made using the ratios of the number of sexually produced individuals to sample size, observed genotypic diversity (Go) to expected genotypic diversity (Ge), and number of genotypes (Ngo) to sample size. Values of Go/Ge much smaller than one indicate the occurrence of clonal reproduction.F-statistics were used to partition genetic variation into that occurring within populations (FIS) and that occurring between populations (FST). To study levels of asexual reproduction and genetic variations occurring within and between populations. Stichopus chloronotus is a common holothurian species on Indo-Pacific coral reefs.

Population genetic structure was studied in two nearshore (Fantome and Great Palm Islands) and two midshelf (Rib and 18-026) reef populations of Holothuria atra on the Great Barrier Reef. Two stations approximately 500 m apart were sampled on each reef (only 150 m apart at Fantome Island due to the limited area in which the species occurs). At each station, 30-40 adult individuals (generally > 50 g) were sampled within a radius of 30m from a marker buoy, in early November 1996. The sampling time in November was chosen to increase the likelihood of finding mature gonads in the sampled animals. Female gonads were dark red, male gonads were orange; several small gonads were examined microscopically to determine whether they were ovaries or testes. Several inidivduals had gonads which were either immature or not detectable, these were exluded from the male/female analyses but included in other analyses.Genetic variation at 5 polymorphic loci was examined using allozyme electrophoresis. The polymorphic enzymes examined were: GPI, HK, LP, PGD and PGM. Measures describing the genetic variables for females, males and unsexed individuals were: sample size per locus; number of alleles per locus; percentage of loci that were polymorphic; heterozygosity (observed=Ho, expected=He); genotypic diversity (observed=Go, expected=Ge, and the ratio of Go to Ge); sample size (Ni); number of genotypes ((observed=Ngo, expected=Nge).Calculation were made on: the number of sexually produced individuals (N); and the ratios of Ngo to Nge; Ni to Ngo; N to Ni.Average weight (g), for females, males and unsexed individuals were recorded; and sex ratios for all sexed individuals and estimated annual fission rates calculated.F-statistics were used to partition genetic variation into that occurring within populations (FIS) and that occurring between populations (FST) for males, females and total individuals for both original and clonal genotype frequencies.A dendrogram was created to show genetic relationships between the populations of the 8 sites using UPGMA cluster algorithm and Nei's unbiased genetic distance. To describe the genetic structures of Holothuria atra using allozyme electrophoresis to quantify the extent of asexual reproduction and to extimate the importance of sexual recruitment in this fissiparous holothurian.

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.