Thomas A. Oliver

Genomic basis for coral resilience to climate change

Recent advances in DNA-sequencing technologies now allow for in-depth characterization of the genomic stress responses of many organisms beyond model taxa. They are especially appropriate for organisms such as reef-building corals, for which dramatic declines in abundance are expected to worsen as anthropogenic climate change intensifies. Different corals differ substantially in physiological resilience to environmental stress, but the molecular mechanisms behind enhanced coral resilience remain unclear. Here, we compare transcriptome-wide gene expression (via RNA-Seq using Illumina sequencing) among conspecific thermally sensitive and thermally resilient corals to identify the molecular pathways contributing to coral resilience. Under simulated bleaching stress, sensitive and resilient corals change expression of hundreds of genes, but the resilient corals had higher expression under control conditions across 60 of these genes. These “frontloaded” transcripts were less up-regulated in resilient corals during heat stress and included thermal tolerance genes such as heat shock proteins and antioxidant enzymes, as well as a broad array of genes involved in apoptosis regulation, tumor suppression, innate immune response, and cell adhesion. We propose that constitutive frontloading enables an individual to maintain physiological resilience during frequently encountered environmental stress, an idea that has strong parallels in model systems such as yeast. Our study provides broad insight into the fundamental cellular processes responsible for enhanced stress tolerances that may enable some organisms to better persist into the future in an era of global climate change.

Do fluctuating temperature environments elevate coral thermal tolerance

In reef corals, much research has focused on the capacity of corals to acclimatize and/or adapt to different thermal environments, but the majority of work has focused on distinctions in mean temperature. Across small spatial scales, distinctions in daily temperature variation are common, but the role of such environmental variation in setting coral thermal tolerances has received little attention. Here, we take advantage of back-reef pools in American Samoa that differ in thermal variation to investigate the effects of thermally fluctuating environments on coral thermal tolerance. We experimentally heat-stressed Acropora hyacinthus from a thermally moderate lagoon pool (temp range 26.5–33.3°C) and from a more thermally variable pool that naturally experiences 2–3xa0h high temperature events during summer low tides (temp range 25.0–35°C). We compared mortality and photosystem II photochemical efficiency of colony fragments exposed to ambient temperatures (median: 28.0°C) or elevated temperatures (median: 31.5°C). In the heated treatment, moderate pool corals showed nearly 50% mortality whether they hosted heat-sensitive (49.2xa0±xa06.5% SE; C2) or heat-resistant (47.0xa0±xa011.2% SE; D) symbionts. However, variable pool corals, all of which hosted heat-resistant symbionts, survived well, showing low mortalities (16.6xa0±xa08.8% SE) statistically indistinguishable from controls held at ambient temperatures (5.1–8.3xa0±xa03.3–8.3% SE). Similarly, moderate pool corals hosting heat-sensitive algae showed rapid rates of decline in algal photosystem II photochemical efficiency in the elevated temperature treatment (slopexa0=xa0−0.04xa0day−1xa0±xa00.007 SE); moderate pool corals hosting heat-resistant algae showed intermediate levels of decline (slopexa0=xa0−0.039xa0day−1xa0±xa00.007 SE); and variable pool corals hosting heat-resistant algae showed the least decline (slopexa0=xa0−0.028xa0day−1xa0±xa00.004 SE). High gene flow among pools suggests that these differences probably reflect coral acclimatization not local genetic adaptation. Our results suggest that previous exposure to an environmentally variable microhabitat adds substantially to coral–algal thermal tolerance, beyond that provided by heat-resistant symbionts alone.

Many corals host thermally resistant symbionts in high-temperature habitat

Physiologically distinct lines of dinoflagellate symbionts, Symbiodinium spp., may confer distinct thermal tolerance thresholds on their host corals. Therefore, if a coral can alternately host distinct symbionts, changes in their Symbiodinium communities might allow corals to better tolerate increasing environmental temperatures. However, researchers are currently debating how commonly coral species can host different symbiont types. We sequenced chloroplast 23xa0s rDNA from the Symbiodinium communities of nine reef-building coral species across two thermally distinct lagoon pools separated by ~500xa0m. The hotter of these pools reaches 35°C in the summer months, while the other pool’s maximum temperature is 1.5°C cooler. Across 217 samples from nine species, we found a single haplotype in both Symbiodinium clades A and D, but four haplotypes in Symbiodinium clade C. Eight of nine species hosted a putatively thermally resistant member of clade D Symbiodinium at least once, one of which hosted this clade D symbiont exclusively. Of the remaining seven that hosted multiple Symbiodinium types, six species showed higher proportions of the clade D symbiont in the hotter pool. Average percentage rise in the frequency of the clade D symbiont from the hotter to cooler pool was 52% across these six species. Even though corals hosted members of both the genetically divergent clades D and C Symbiodinium, some showed patterns of host–symbiont specificity within clade C. Both Acropora species that hosted clade C exclusively hosted a member of sub-clade C2, while all three Pocillopora species hosted a member of sub-clade C1 (sensu van Oppen et al. 2001). Our results suggest that coral–algal symbioses often conform to particular temperature environments through changes in the identity of the algal symbiont.

Coral-associated marine fungi form novel lineages and heterogeneous assemblages

Coral stress tolerance is intricately tied to the animals association with microbial symbionts. The most well-known of these symbioses is that between corals and their dinoflagellate photobionts (Symbiodinium spp.), whose genotype indirectly affects whether a coral can survive cyclical and anthropogenic warming events. Fungi comprise a lesser-known coral symbiotic community whose taxonomy, stability and function is largely un-examined. To assess how fungal communities inside a coral host correlate with water temperature and the genotype of co-occurring Symbiodinium, we sampled Acropora hyacinthus coral colonies from adjacent natural pools with different water temperatures and Symbiodinium identities. Phylogenetic analysis of coral-associated fungal ribosomal DNA amplicons showed a high diversity of Basidiomycetes and Ascomycetes, including several clades separated from known fungal taxa by long and well-supported branches. Community similarity did not correlate with any measured variables, and total fungal community composition was highly variable among A. hyacinthus coral colonies. Colonies in the warmer pool contained more phylogenetically diverse fungal communities than the colder pool and contained statistically significant ‘indicator’ species. Four taxa were present in all coral colonies sampled, and may represent obligate associates. Messenger RNA sequenced from a subset of these same colonies contained an abundance of transcripts involved in metabolism of complex biological molecules. Coincidence between the taxonomic diversity found in the DNA and RNA analysis indicates a metabolically active and diverse resident marine fungal community.

Lineage-Specific Transcriptional Profiles of Symbiodinium spp. Unaltered by Heat Stress in a Coral Host

Dinoflagellates of the genus Symbiodinium form an endosymbiosis with reef building corals, in which photosynthetically derived nutrients comprise the majority of the coral energy budget. An extraordinary amount of functional and genetic diversity is contained within the coral-associated Symbiodinium, with some phylotypes (i.e., genotypic groupings), conferring enhanced stress tolerance to host corals. Recent advances in DNA sequencing technologies have enabled transcriptome-wide profiling of the stress response of the cnidarian coral host; however, a comprehensive understanding of the molecular response to stress of coral-associated Symbiodinium, as well as differences among physiologically susceptible and tolerant types, remains largely unexplored. Here, we examine the transcriptome-wide response to heat stress via RNA-Seq of two types of Symbiodinium, the putatively thermotolerant type D2 and the more susceptible type C3K, resident within the same coral host species, Acropora hyacinthus. Contrary to previous findings with coral hosts, we find no detectable change in gene expression across the dinoflagellate transcriptome after 3 days of elevated thermal exposure, despite physical evidence of symbiosis breakdown. However, hundreds of genes identified as orthologs between the C and D types exhibited significant expression differences within treatments (i.e., attributable solely to type, not heat exposure). These include many genes related to known thermotolerance mechanisms including heat shock proteins and chloroplast membrane components. Additionally, both the between-treatment similarities and between-type differences remained pervasive after 12-18 months of common garden acclimation and in mixed Symbiodinium assemblages within the same coral host colony.

A Method for Detecting Population Genetic Structure in Diverse, High Gene-Flow Species

Detecting small amounts of genetic subdivision across geographic space remains a persistent challenge. Often a failure to detect genetic structure is mistaken for evidence of panmixia, when more powerful statistical tests may uncover evidence for subtle geographic differentiation. Such slight subdivision can be demographically and evolutionarily important as well as being critical for management decisions. We introduce here a method, called spatial analysis of shared alleles (SAShA), that detects geographically restricted alleles by comparing the spatial arrangement of allelic co-occurrences with the expectation under panmixia. The approach is allele-based and spatially explicit, eliminating the loss of statistical power that can occur with user-defined populations and statistical averaging within populations. Using simulated data sets generated under a stepping-stone model of gene flow, we show that this method outperforms spatial autocorrelation (SA) and Phi(ST) under common real-world conditions: at relatively high migration rates when diversity is moderate or high, especially when sampling is poor. We then use this method to show clear differences in the genetic patterns of 2 nearshore Pacific mollusks, Tegula funebralis (= Chlorostoma funebralis) and Katharina tunicata, whose overall patterns of within-species differentiation are similar according to traditional population genetics analyses. SAShA meaningfully complements Phi(ST)/F(ST), SA, and other existing geographic genetic analyses and is especially appropriate for evaluating species with high gene flow and subtle genetic differentiation.

Whole-Genome Positive Selection and Habitat-Driven Evolution in a Shallow and a Deep-Sea Urchin

Comparisons of genomic sequence between divergent species can provide insight into the action of natural selection across many distinct classes of proteins. Here, we examine the extent of positive selection as a function of tissue-specific and stage-specific gene expression in two closely-related sea urchins, the shallow-water Strongylocentrotus purpuratus and the deep-sea Allocentrotus fragilis, which have diverged greatly in their adult but not larval habitats. Genes that are expressed specifically in adult somatic tissue have significantly higher dN/dS ratios than the genome-wide average, whereas those in larvae are indistinguishable from the genome-wide average. Testis-specific genes have the highest dN/dS values, whereas ovary-specific have the lowest. Branch-site models involving the outgroup S. franciscanus indicate greater selection (ωFG) along the A. fragilis branch than along the S. purpuratus branch. The A. fragilis branch also shows a higher proportion of genes under positive selection, including those involved in skeletal development, endocytosis, and sulfur metabolism. Both lineages are approximately equal in enrichment for positive selection of genes involved in immunity, development, and cell–cell communication. The branch-site models further suggest that adult-specific genes have experienced greater positive selection than those expressed in larvae and that ovary-specific genes are more conserved (i.e., experienced greater negative selection) than those expressed specifically in adult somatic tissues and testis. Our results chart the patterns of protein change that have occurred after habitat divergence in these two species and show that the developmental or functional context in which a gene acts can play an important role in how divergent species adapt to new environments.

Restriction Site Tiling Analysis: accurate discovery and quantitative genotyping of genome-wide polymorphisms using nucleotide arrays

High-throughput genotype data can be used to identify genes important for local adaptation in wild populations, phenotypes in lab stocks, or disease-related traits in human medicine. Here we advance microarray-based genotyping for population genomics with Restriction Site Tiling Analysis. The approach simultaneously discovers polymorphisms and provides quantitative genotype data at 10,000s of loci. It is highly accurate and free from ascertainment bias. We apply the approach to uncover genomic differentiation in the purple sea urchin.

The role of genes in understanding the evolutionary ecology of reef building corals

A key tool in evolutionary ecology is information about the temporal dynamics of species over time. Paleontology has long been the major source of this information, however, a very different source of temporal data resides in the variation of genes within and between species. These data provide an independent way to date species divergence but can also uniquely reveal processes such as gene introgression between species and demographic isolation within species. Genetic tools are particularly useful for understanding genera with closely related species that can potentially hybridize, such as reef building corals. Here we use genetic data from four loci (3 introns and 1 mitochondrial) to assay divergence and gene flow in Caribbean corals. The data show that there is persistent gene flow between species in the genus Acropora, but that this gene flow is unidirectional and highly variable among loci. Selection against introgressed alleles is high enough at one locus, Mini-collagen, to prevent gene flow between species. By contrast, selection against mitochondrial introgression appears much weaker, with 40–80 times higher rates of inter-specific gene flow than for any nuclear locus we examined. The same loci also show that gene flow among locations within species is locally restricted, but is nevertheless much higher between populations than between species. Interpretation of population data is complicated by the variable nature of selection on introgressed alleles, and some patterns of genetic differentiation might be driven by local introgression and selection. The combination of inter-specific and intra-specific data using the same loci treated in a genealogical framework helps resolve complications due to introgression and helps paint a picture of the evolution and maintenance of species in a complex spatial and temporal framework.