I am currently a Postdoctoral Research Fellow in the ToBo lab on Moku O Loʻe (Coconut Island) at the Hawaii Institute of Marine Biology. My research predominantly focuses on species connectivity across the Hawaiian Archipelago, relating those patterns to environmental predictors to inform management decisions. As different phyla and species have different life histories, to better understand these breaks between the islands we're currently looking a number of species across multiple phyla including fish (e.g. Mulloides flavolineatus), crustaceans (e.g. Panulirus penicillatus and Panulirus marginatus), starfish (Acanthaster planci), coral (Pocillopora meandrina, Montipora capitata and Porites lobata) and we'll be adding more in the future.
To do this we're using next generation sequencing techniques and a library preparation developed in the lab called ezRAD. ezRAD is from the family of RAD (restriction site associated DNA) techniques that cuts up the DNA (either by sonication or restriction enzymes) and looks at large areas of the genome, as apposed to the whole genome. RADseq data often forms stacks of DNA on the same loci (vertical coverage of the genome). These stacks are then used to find SNPs or single-nucleotide polymorphisms. The interesting difference with ezRAD compared to other RAD techniques is that it utilizes a frequent cutting enzyme and so the data produced not only forms vertical stacks but also horizontal coverage across other regions of the genome. This makes the data more tricky to analyse, but it does mean that using this technique we can get almost 100% of the mitochondrial genome, ribosomes and histones (i.e. those high copy regions).
See below for the ezRAD protocol. It's an ever changing document as we improve the technique, and feel free to contact me if you have questions about it.
I'm also working with Dr Zac Forsman on the Coconut Island Coral Nursery, which was built in 2017 from recycled materials salvaged from retired fish and dolphin pens. During this recycling project we also recovered 100's corals from these pens through the help of DAR and volunteers. With these corals we plan to develop a work-flow to help rebuild coral reefs and their associated fisheries in Hawai'i. We plan on doing this through empirical testing and various techniques including a micro-fragmentation. This technique involves cutting corals into smaller pieces and attaching them to larger surfaces so that when they grow they'll fuse together and form a larger colony a lot quicker than if we just housed the original fragments in the nursery. Developing the right kind of surfaces to grow these corals is also very important and we also hope to develop seedling modules that can be deployed without using SCUBA. We have already, and will continue to work with volunteers and schools to not only help us, but teach them the importance of coral reefs, which sustain a complex and diverse community of organisms, as well as providing coastal protection.
Mahalo
To do this we're using next generation sequencing techniques and a library preparation developed in the lab called ezRAD. ezRAD is from the family of RAD (restriction site associated DNA) techniques that cuts up the DNA (either by sonication or restriction enzymes) and looks at large areas of the genome, as apposed to the whole genome. RADseq data often forms stacks of DNA on the same loci (vertical coverage of the genome). These stacks are then used to find SNPs or single-nucleotide polymorphisms. The interesting difference with ezRAD compared to other RAD techniques is that it utilizes a frequent cutting enzyme and so the data produced not only forms vertical stacks but also horizontal coverage across other regions of the genome. This makes the data more tricky to analyse, but it does mean that using this technique we can get almost 100% of the mitochondrial genome, ribosomes and histones (i.e. those high copy regions).
See below for the ezRAD protocol. It's an ever changing document as we improve the technique, and feel free to contact me if you have questions about it.
I'm also working with Dr Zac Forsman on the Coconut Island Coral Nursery, which was built in 2017 from recycled materials salvaged from retired fish and dolphin pens. During this recycling project we also recovered 100's corals from these pens through the help of DAR and volunteers. With these corals we plan to develop a work-flow to help rebuild coral reefs and their associated fisheries in Hawai'i. We plan on doing this through empirical testing and various techniques including a micro-fragmentation. This technique involves cutting corals into smaller pieces and attaching them to larger surfaces so that when they grow they'll fuse together and form a larger colony a lot quicker than if we just housed the original fragments in the nursery. Developing the right kind of surfaces to grow these corals is also very important and we also hope to develop seedling modules that can be deployed without using SCUBA. We have already, and will continue to work with volunteers and schools to not only help us, but teach them the importance of coral reefs, which sustain a complex and diverse community of organisms, as well as providing coastal protection.
Mahalo