Coral reefs worldwide are severely threatened by climate change, and about the only thing that can save them is coral adaptation to the new climate conditions. But can corals adapt, and if yes, how rapidly? This is one of the most critical unknowns in reef conservation planning, very difficult to assess experimentally because the timescales involved are most likely decades or even hundreds of years. Our idea is to look into the past: using state-of-the-art genomics, we will reconstruct the rises and falls of Caribbean reefs in response to past climate changes over the last 100,000 years.
This information will allow us to choose the best strategy to save the corals for the future. If adaptation in corals tends to be slow, resulting in dramatic population declines during climate change events, we must start thinking on regional and long-term scales and put a lot more effort into identifying and preserving reefs that could serve as coral safe houses ("refugia"). Such locations would later become seeders to repopulate devastated reefs, ensuring long-term persistence of corals. If, on the other hand, corals tended to survive through past climate swings relatively unscathed, our best strategy would be to focus on mitigation of local threats, such as land-based pollution and overfishing.
Genetic diversity and population size are inherently linked, so that rises and falls of populations in the past are recorded in patterns of mutations in the genome. To reconstruct these changes, we will sequence genomes of two key reef-building coral species in the Caribbean, the great star coral Montastrea cavernosa and the round starlet coral Siderastrea siderea.
The great star coral is one of the most easily recognizable Caribbean mound-shaped corals because of its very large round polyps. It prefers to grow in offshore and deep reef habitats, where it often reaches massive sizes and contributes significantly to the reef's structural framework, which is why we chose this species for the project. One curious feature of this coral is its colorful fluorescence, which gives colonies a range of color varieties from red to blue. The great star coral has separate sexes - a single coral colony can be a boy or a girl.
The round starlet coral is remarkable in its resiliency, which is why we selected this species alongside the more ecologically "choosy" great star coral. It can be found essentially in all Caribbean reef habitats, from deep offshore reefs to shallow hardbottom patches right next to shore. It is one of the few Caribbean coral species that appears to be thriving despite region-wide reef decline, and could be one of the ultimate climate change survivors. It is easily recognizable by its rounded shape, smooth surface with dimple-like polyps and somewhat purplish tinge. Just like the great star coral, a round starlet coral colony can be a boy or a girl.
In addition to unlocking corals’ past, genome sequence can elucidate virtually any other aspect of coral biology. We are therefore committed to making the newly sequenced genomes immediately available to the research community for unconditional use, so that anyone with a good idea how to save the reefs will have the best information resource at their disposal.
Only ten years ago sequencing multiple genomes would have required multi-million dollar grants and international consortia, but thanks to major breakthroughs in DNA sequencing and genome analysis methods the entire project can be performed here at UT. The cost of sequencing a novel genome has dropped dramatically, and UT has all the necessary instrumentation and technical support at its Genomic Sequencing and Analysis Facility. The computational needs of the project are fully met by high-performance computer clusters of the Texas Advanced Computer Center. Last but not least, we have accumulated nearly ten years of experience in bioinformatics and genomics since our lab has been established at UT. With your help, our team will now be able to bring full power of modern genomics to forecast the future of Caribbean coral reefs.
To obtain genomic data suitable for reconstructing population histories, we will supplement the now-typical massively parallel short read genome sequencing with Hi-C (pronounced “high sea”) method, a novel approach to assemble individual chromosomes. These data will be analyzed using multiple sequential Markovian coalescent (MSMC), a sophisticated procedure originally developed to reconstruct human expansions throughout the globe. MSMC analyzes distances between mutations throughout the genome and will be able to infer rises and falls of Caribbean coral populations between 5,000 and 100,000 years ago. To reconstruct more recent changes, we will use the low-cost genotyping method called 2bRAD ("to be rad", developed in our lab) to process more coral colonies. These data will be analyzed using dadi , the method that infers recent changes in population size from patterns of present-day genetic variation.
We wish to thank Jeff Mertz and Kelly O'Neill who helped us to put together our video. We are especially grateful to Guy and Anita Chaumette of the Liquid Motion Film for contributing the opening reef footage.
NOTE: All the coral fragments featured in our video are leftovers from past experiments in Matz lab, obtained under appropriate research permits. Never, ever purchase a natural coral for decoration purposes.
Genomic DNA sample preparation for one coral
Genotyping of one coral sample using 2bRAD method.
Hi-C sample preparation for one coral.
Improve genome data quality from draft (15x coverage) to advanced (30x coverage) for one coral species.
Hi-C analysis for one coral species.
Improve genome data quality from advanced (30x coverage) to excellent (60x coverage) for one coral species.
Re-sequencing genome in another individual of the same species to improve precision of population size reconstruction.
Draft genome sequencing for one coral species.
Fully funds all genomic work for one coral species. This contribution will be personally acknowledged in forthcoming scientific papers.