Luke Thomas

Exploring Symbiodinium diversity and host specificity in Acropora corals from geographical extremes of Western Australia with 454 amplicon pyrosequencing

Scleractinian corals have demonstrated the ability to shuffle their endosymbiotic dinoflagellate communities (genus Symbiodinium) during periods of acute environmental stress. This has been proposed as a mechanism of acclimation, which would be increased by a diverse and flexible association with Symbiodinium. Conventional molecular techniques used to evaluate Symbiodinium diversity are unable to identify genetic lineages present at background levels below 10%. Next generation sequencing (NGS) offers a solution to this problem and can resolve microorganism diversity at much finer scales. Here we apply NGS to evaluate Symbiodinium diversity and host specificity in Acropora corals from contrasting regions of Western Australia. The application of 454 pyrosequencing allowed for detection of Symbiodinium operational taxonomic units (OTUs) occurring at frequencies as low as 0.001%, offering a 10 000‐fold increase in sensitivity compared to traditional methods. All coral species from both regions were overwhelmingly dominated by a single clade C OTU (accounting for 98% of all recovered sequences). Only 8.5% of colonies associated with multiple clades (clades C and D, or C and G), suggesting a high level of symbiont specificity in Acropora assemblages in Western Australia. While only 40% of the OTUs were shared between regions, the dominance of a single OTU resulted in no significant difference in Symbiodinium community structure, demonstrating that the coral‐algal symbiosis can remain stable across more than 15° of latitude and a range of sea surface temperature profiles. This study validates the use of NGS platforms as tools for providing fine‐scale estimates of Symbiodinium diversity and can offer critical insight into the flexibility of the coral‐algal symbiosis.

Resilience to disturbance despite limited dispersal and self-recruitment in tropical barrel sponges: Implications for conservation and management

While estimates of connectivity are important for effective management, few such estimates are available for reef invertebrates other than for corals. Barrel sponges are one of the largest and most conspicuous members of the coral reef fauna across the Indo-Pacific and given their large size, longevity and ability to process large volumes of water, they have a major role in reef functioning. Here we used a panel of microsatellite markers to characterise the genetic structure of two barrel sponge species, Xestospongia testudinaria and a currently undescribed Xestospongia species. We sampled across seven populations in the Wakatobi Marine National Park, SE Sulawesi (Indonesia) spanning a spatial scale of approximately 2 to 70 km, and present the first estimates of demographic connectivity for coral reef sponges. Genetic analyses showed high levels of genetic differentiation between all populations for both species, but contrasting patterns of genetic structuring for the two species. Autocorrelation analyses showed the likely dispersal distances of both species to be in the order of 60 and 140 m for Xestopongia sp. and Xestospongia testudinaria, respectively, which was supported by assignment tests that showed high levels of self-recruitment (>80%). We also found consistently high inbreeding coefficients across all populations for both species. Our study highlights the potential susceptibility of barrel sponges to environmental perturbations because they are generally long-lived, slow growing, have small population sizes and are likely to be reliant on self-recruitment. Surprisingly, despite these features we actually found the highest abundance of both barrel sponge species (although they were generally smaller) at a site that has been severely impacted by humans over the last fifty years. This suggests that barrel sponges exhibit environmental adaptation to declining environmental quality and has important implications for the management and conservation of these important reef species.

Isolation by resistance across a complex coral reef seascape.

A detailed understanding of the genetic structure of populations and an accurate interpretation of processes driving contemporary patterns of gene flow are fundamental to successful spatial conservation management. The field of seascape genetics seeks to incorporate environmental variables and processes into analyses of population genetic data to improve our understanding of forces driving genetic divergence in the marine environment. Information about barriers to gene flow (such as ocean currents) is used to define a resistance surface to predict the spatial genetic structure of populations and explain deviations from the widely applied isolation-by-distance model. The majority of seascape approaches to date have been applied to linear coastal systems or at large spatial scales (more than 250 km), with very few applied to complex systems at regional spatial scales (less than 100 km). Here, we apply a seascape genetics approach to a peripheral population of the broadcast-spawning coral Acropora spicifera across the Houtman Abrolhos Islands, a high-latitude complex coral reef system off the central coast of Western Australia. We coupled population genetic data from a panel of microsatellite DNA markers with a biophysical dispersal model to test whether oceanographic processes could explain patterns of genetic divergence. We identified significant variation in allele frequencies over distances of less than 10 km, with significant differentiation occurring between adjacent sites but not between the most geographically distant ones. Recruitment probabilities between sites based on simulated larval dispersal were projected into a measure of resistance to connectivity that was significantly correlated with patterns of genetic divergence, demonstrating that patterns of spatial genetic structure are a function of restrictions to gene flow imposed by oceanographic currents. This study advances our understanding of the role of larval dispersal on the fine-scale genetic structure of coral populations across a complex island system and applies a methodological framework that can be tailored to suit a variety of marine organisms with a range of life-history characteristics.

Restricted gene flow and local adaptation highlight the vulnerability of high-latitude reefs to rapid environmental change

Global climate change poses a serious threat to the future health of coral reef ecosystems. This calls for management strategies that are focused on maximizing the evolutionary potential of coral reefs. Fundamental to this is an accurate understanding of the spatial genetic structure in dominant reef-building coral species. In this study, we apply a genotyping-by-sequencing approach to investigate genome-wide patterns of genetic diversity, gene flow, and local adaptation in a reef-building coral, Pocillopora damicornis, across 10 degrees of latitude and a transition from temperate to tropical waters. We identified strong patterns of differentiation and reduced genetic diversity in high-latitude populations. In addition, genome-wide scans for selection identified a number of outlier loci putatively under directional selection with homology to proteins previously known to be involved in heat tolerance in corals and associated with processes such as photoprotection, protein degradation, and immunity. This study provides genomic evidence for both restricted gene flow and local adaptation in a widely distributed coral species, and highlights the potential vulnerability of leading-edge populations to rapid environmental change as they are locally adapted, reproductively isolated, and have reduced levels of genetic diversity.

Isolation and characterisation of twelve polymorphic microsatellite markers for Xestospongia spp. and their use for confirming species identity

Barrel sponges are one of the largest and most conspicuous members of the coral reef fauna across the Indo-Pacific that are under threat from habitat degradation. Twelve novel microsatellite markers were developed for Xestospongia testudinaria from 454 sequence data and scored across 47 individual barrel sponges collected from the Sampela reef in the Wakatobi Marine National Park, Indonesia. All loci except one was polymorphic with the number of alleles per locus ranging from 5 to 24. Observed heterozygosity ranged from 0.08 to 0.77 and FIS values ranged from −1.61 to 0.77, with the majority of loci being in Hardy–Weinberg equilibrium (HWE). We then tested our markers on 28 likely Xestospongia bergquistia specimens from the same reef. Observed heterozygosity ranged from 0.23 to 0.593 and FIS values ranged from −0.078 to 0.373; all but two loci were in HWE. Furthermore, we confirmed the differentiation of these two species by Principle Coordinate Analysis and Analysis of Molecular Variance. These markers will be useful for a range of future fine-scale population genetics studies for these two important reef species.

Genomic signatures of local adaptation reveal source-sink dynamics in a high gene flow fish species.

Understanding source-sink dynamics is important for conservation management, particularly when climatic events alter species’ distributions. Following a 2011 ‘marine heatwave’ in Western Australia, we observed high recruitment of the endemic fisheries target species Choerodon rubescens, towards the cooler (southern) end of its distribution. Here, we use a genome wide set of 14 559 single-nucleotide polymorphisms (SNPs) to identify the likely source population for this recruitment event. Most loci (76%) showed low genetic divergence across the species’ range, indicating high levels of gene flow and confirming previous findings using neutral microsatellite markers. However, a small proportion of loci showed strong patterns of differentiation and exhibited patterns of population structure consistent with local adaptation. Clustering analyses based on these outlier loci indicated that recruits at the southern end of C. rubescens’ range originated 400 km to the north, at the centre of the species’ range, where average temperatures are up to 3 °C warmer. Survival of these recruits may be low because they carry alleles adapted to an environment different to the one they now reside in, but their survival is key to establishing locally adapted populations at and beyond the range edge as water temperatures increase with climate change.

The genomics of recovery from coral bleaching

Ecological damage from periodic environmental extremes is often repaired in resilient ecosystems, but the rate of return to a non-damaged state is critical. Measures of recovery of communities include biomass, productivity and diversity, while measures of recovery of individuals tend to focus on physiological conditions and the return to normal metabolic functioning. Transcriptomics offers a window into the entire physiology of the organism under stress and can represent a holistic view of organismal recovery. In this study, we track the recovery of seven colonies of Acropora hyacinthus following a natural bleaching event. We identified a large environmental stress response in the field that involved approximately 20% of the host transcriptome. The transcriptome remained largely perturbed for at least six months after temperatures had cooled and four months after symbiont populations had recovered. Moreover, a small set of genes did not recover to previous expression levels even 12 months after the event, about the time that normal growth rates resumed. This study is among the first to incorporate transcriptomics into a longitudinal dataset of recovery from environmental stress. The data demonstrate large and lasting effects on coral physiology long after environmental conditions return to normal and symbiont populations recover.

Phylogenomics provides new insight into evolutionary relationships and genealogical discordance in the reef-building coral genus Acropora

Understanding the genetic basis of reproductive isolation is a long-standing goal of speciation research. In recently diverged populations, genealogical discordance may reveal genes and genomic regions that contribute to the speciation process. Previous work has shown that conspecific colonies of Acropora that spawn in different seasons (spring and autumn) are associated with highly diverged lineages of the phylogenetic marker PaxC. Here, we used 10 034 single-nucleotide polymorphisms to generate a genome-wide phylogeny and compared it with gene genealogies from the PaxC intron and the mtDNA Control Region in 20 species of Acropora, including three species with spring- and autumn-spawning cohorts. The PaxC phylogeny separated conspecific autumn and spring spawners into different genetic clusters in all three species; however, this pattern was not supported in two of the three species at the genome level, suggesting a selective connection between PaxC and reproductive timing in Acropora corals. This genome-wide phylogeny provides an improved foundation for resolving phylogenetic relationships in Acropora and, combined with PaxC, provides a fascinating platform for future research into regions of the genome that influence reproductive isolation and speciation in corals.

A fluorescence-based quantitative real-time PCR assay for accurate Pocillopora damicornis species identification

Pocillopora damicornis is one of the most extensively studied coral species globally, but high levels of phenotypic plasticity within the genus make species identification based on morphology alone unreliable. As a result, there is a compelling need to develop cheap and time-effective molecular techniques capable of accurately distinguishing P. damicornis from other congeneric species. Here, we develop a fluorescence-based quantitative real-time PCR (qPCR) assay to genotype a single nucleotide polymorphism that accurately distinguishes P. damicornis from other morphologically similar Pocillopora species. We trial the assay across colonies representing multiple Pocillopora species and then apply the assay to screen samples of Pocillopora spp. collected at regional scales along the coastline of Western Australia. This assay offers a cheap and time-effective alternative to Sanger sequencing and has broad applications including studies on gene flow, dispersal, recruitment and physiological thresholds of P. damicornis.

Severe loss of anemones and anemonefishes from a premier tourist attraction at the Houtman Abrolhos Islands, Western Australia

The Houtman Abrolhos Islands (29° 00′ S) are the southernmost coral reefs in the Indian Ocean, located 60 km off central Western Australia. The “Anemone Lump”, a 185×400 m reef that rises steeply from 38 m to 4 m, is the premier dive site at the Islands, with a dedicated underwater tourist trail. The site is a fish habitat protection area and tourist attraction due to its abundance of anemones (Entacmaea quadricolor) and anemonefish (Amphiprion clarkii). Photographic evidence and diver observations documented that in 1992, anemone cover exceeded 70 % (Fig. 1a) and supported hundreds of Clark’s anemonefish. By October 2012, no anemones or anemonefishes could be found despite intensive searching over an area of 2,500 m. The site, once renowned for being covered in anemones, is now covered predominantly by Sargassum and plating Acropora spicifera (Fig. 1b). The loss of anemonefishes is most likely due to the loss of anemones, but the reason(s) for the loss of anemones is unknown. Elevated sea temperatures can bleach and kill Entacmaea quadricolor (Hill and Scott 2012), and declines in abundance have occurred at various locations in association with coral bleaching events (Hobbs et al. 2013). Anemones were present before the “marine heat wave” of 2011, which caused widespread coral bleaching across the Houtman Albrolhos Islands (Abdo et al. 2012). However, it is also likely that factors other than elevated sea temperatures have contributed to loss of anemones as anecdotal reports indicate the decline in anemones has occurred over the last 20 years.