Knowledge of genetic markers that are correlated to stress tolerance may improve spatial mapping of reef vulnerability and can inform restoration efforts, including the choice of genotypes for breeding and reseeding. During my post-doctoral research at AIMS, I explored various methods for screening transcriptome data for candidate genetic markers in the reef building corals Acropora millepora and Pocillopora damicornis (types α and β).
In A. millepora, Single Nucleotide Polymorphisms (SNPs) were pre-selected by targeting genes believed to be involved in the coral thermal stress responses. In P. damicornis (types α and β), SNPs showing varying allele frequencies between two populations from distinct environments were pre-selected. Allele frequencies at nine, five and eight of the pre-selected SNP loci were correlated against gradients of water clarity and temperature in a large number of populations along the Great Barrier Reef.
A significant correlation between environmental category and SNP allele frequency was detected in up to 55% of the tested loci, which is an exceptional success rate for these types of tests. In P. damicornis, SNP allele frequencies of β-hexosaminidase and Elongation factor 1-α were significantly correlated to temperature in type α and to temperature and/or water clarity respectively in type β. Type α also showed a correlation between water clarity and SNP allele frequency in a gene of unknown function. In A. millepora, allele frequencies at five (α-gamma crystallin, Galaxin, UbiquitinLigand of Numb X2 and Thioredoxin) SNP loci showed significant correlations. (Full Text)
At present, my Ph.D. student is validating these and a range of additional SNP markers through laboratory or field assessment of relative stress tolerance of colonies harbouring different alleles. It is anticipated that a proportion of these markers may represent the first coral candidate Quantitative Trait Loci for environmental stress tolerance and provide an important genetic tool that can be incorporated into spatial management decisions and restoration efforts of coral reefs. One pertinent example would be to combine spatial data of tolerant populations with genetic connectivity and thus identify high priority conservation reefs and implement targeted coral husbandry and active restoration efforts that use locally- and stress-adapted genotypes.
The Reef Futures Genomics consortium brings together leading institutions in coral reef science and management, including the Great Barrier Reef Foundation, James Cook University, the Australian Institute of Marine Science, the University of Queensland, the Great Barrier Reef Marine Park Authority, the King Abdullah University of Science and Technology (Saudi Arabia) and the Australian National University.
I am one of the founding members of this consortium and act as a liaison and translator of the research outcomes to the end user (GBRMPA) as well as providing advice to the researchers on end use relevance and strategic research priorities. I provide input into various research proposals, such as the Queensland Government accelerated partnership program and linked ARC Discover grant applications.
The impact of a mass bleaching event on temporal and spatial population genetic structure in four scleractinian coral species in the Acropora aspera group was studied around the Palm Island group in the central Great Barrier Reef. Species status of sympatric populations of two of the four species, A. millepora and A. spathulata, was confirmed by the population genetic data; these species have recently been separated based on morphological and breeding characters.
Spatial analyses of population samples from 2004 detected differences in the level of gene flow among locations. No significant genetic differentiation was inferred between conspecific populations at Orpheus and Pelorus Islands, which are both located in the northern part of the island group and separated by ~1000 m.
In contrast, all populations at Fantome Island were genetically differentiated, despite being located only 11km to the South. Sampling of A. millepora and A. pulchra, in the year prior to the 1998 mass bleaching event enabled a temporal comparison across this event. The genetic composition of these populations changed between 1997 and 2004, but patterns of genetic differentiation among locations were similar to those found in 2004.
Extensive mortality of these species following the 1998 bleaching event did not cause an apparent reduction in genetic diversity and identical multi-locus genotypes were encountered in both temporal samples, suggesting re-growth of surviving genotypes contributed to the recovery of these populations. Comparisons among the four study species revealed lower genetic diversity in A. papillare, consistent with its low abundance throughout its distributional range
Project Kimberley is a consortium of scientists, landholders, community groups, and government agencies who are working to understand and mitigate the impact of cane toads across the Kimberley. We are currently undertaking long-term monitoring of native fauna to produce baseline information that will be used to assess which Kimberley species are most affected by the toads. Part of this effort involves developing research programs that document the ecology and genetics of the most affected species. That data will be important for recovery plans as the Kimberley adjusts to the presence of the toad.
My role in this project is to design the spatial collection of tissue samples and then to generate and analyse the population genetic data. For this project we are using genome wide SNP analysis generated through a recently developed RAD tag sequencing method. I also provide input and the majority of the text for the genetics component of any major research grant application within the scope of this program, such as ARC discovery and linkage grants.
My Ph.D. research focused on assessing species boundaries, genetic diversity and population genetic structures of two species of scleractinian corals within and among marine protected areas in the Western Indian Ocean.
The results are all published in peer reviewed journals and will assist with the future design and location of MPAs for coral reef management in East Africa.
