NHGRI Postdoctoral Research Fellowship

My current research at the National Institutes of Health (NIH) in the National Human Genome Research Institute (NHGRI) is working to assemble and annotate a reference genome for the hydrozoan Podocoryna carnea, an emerging model for studies of striated muscle evolution and regeneration. Next, we will seek to create single-cell atlases of all cell types present in different Podocoryna life stages.

Podocoryna carnea is an emerging cnidarian model species. Colonies of polyps are grown on microscope slides, and release medusae (jellyfish) that possess striated muscle tissues into the water column.
Podocoryna carnea is an emerging cnidarian model species. Colonies of polyps are grown on microscope slides, and release medusae (jellyfish) that possess striated muscle tissues into the water column.

Smithsonian Biodiversity Genomics Fellowship

I am especially interested in how these host-microbe interactions affect the ecology, evolution, and biodiversity of tropical coral reef and other marine ecosystems. In particular, I am fascinated by scleractinian corals in the genus Pocillopora because of their ecological importance, large geographic distribution, and complex microbial symbioses. Another aim of my research is to use genomics to resolve the systematics of this important coral genus, and apply metagenomics to assess signatures of host-microbe coevolution among Pocillopora corals and their associated symbiont communities.

My previous postdoctoral research applied genomics to delimit Pocillopora coral species and re-assess the morphology-based taxonomy for this important and widespread coral genus, focusing on the eastern tropical Pacific (ETP). I am continuing to work with teams at the National Museum of Natural History (NMNH) in the Invertebrate Zoology (IZ) department’s Coral Lab and the Smithsonian Tropical Research Institute (STRI).

Smithsonian research facilities at STRI and NMNH. The STRI Naos Island Marine Lab grants access to coral monitoring sites in the eastern Pacific, and the NMNH IZ department has an immense specimen collection and cutting-edge molecular laboratories.
Smithsonian research facilities at STRI and NMNH. The STRI Naos Island Marine Lab grants access to coral monitoring sites in the eastern Pacific, and the NMNH IZ department has an immense specimen collection and cutting-edge molecular laboratories.

The Smithsonian’s research platform in Panamá and Washington are key for this project. The Naos Marine & Molecular Laboratories are an excellent launch point to several field sites in the ETP that span a gradient of seasonal wind-driven upwelling from Isla Coiba in the Gulf of Chiriquí to Isla Saboga in the Gulf of Panamá. Field-collected Pocillopora coral samples from these sites have been transported to the NMNH for genomic and morphometric species delimitation analyses and comparisons to historical Pocillopora specimens in the IZ department collections.

SI BioG project summary. (A) The Pocillopora coral holobiont comprises the coral host and symbiotic algae and bacteria, some of which are transmitted between host generations. (B) Phylosymbiosis occurs when the relationships between symbiotic microbial communities recapitulate host phylogenetic relationships. (C) Coral branch morphology and corallite microstructure for three Pocillopora species last revised in Schmidt-Roach et al. (2014), correspondence between genetics and morphological characters has not been assessed for the eight morphospecies that are present in Panamá. (D) Location of STRI coral monitoring sites in the Gulf of Chiriquí and Gulf of Panamá. (E) Locations and numbers of preserved Pocillopora coral specimens in the NMNH Invertebrate Zoology collections.
SI BioG project summary. (A) The Pocillopora coral holobiont comprises the coral host and symbiotic algae and bacteria, some of which are transmitted between host generations. (B) Phylosymbiosis occurs when the relationships between symbiotic microbial communities recapitulate host phylogenetic relationships. (C) Coral branch morphology and corallite microstructure for three Pocillopora species last revised in Schmidt-Roach et al. (2014), correspondence between genetics and morphological characters has not been assessed for the eight morphospecies that are present in Panamá. (D) Location of STRI coral monitoring sites in the Gulf of Chiriquí and Gulf of Panamá. (E) Locations and numbers of preserved Pocillopora coral specimens in the NMNH Invertebrate Zoology collections.

My hope is that an improved taxonomy of these critical coral species will be a valuable resource for scientists studying coral reef species distributions and interactions in marginal ecosystems and will reveal the fundamental co-evolutionary processes that help generate coral species diversity in other eco-regions.

Ph.D. research on Pocillopora host-microbe interactions

I completed my Ph.D. at the University of Miami Rosenstiel School of Marine and Atmospheric Science (RSMAS), working in the Cnidarian Immunity Laboratory with Dr. Nikki Traylor-Knowles as my Ph.D. advisor.

During my Ph.D. I completed an NSF East Asia and Pacific Summer Institutes (EAPSI) fellowship in Taiwan, where I studied Pocillopora coral gene expression and bacteria community shifts in response to experimental treatments with bacteria lipopolysaccharide, antibiotics, and heat stress that were intended to disrupt normal host-bacteria interactions. The publications that resulted from these experiments can be found here and here.

NSF EAPSI corals and sites. Pocillopora acuta colonies at Outlet reef (top) and Wanglitung reef (bottom) near Kenting, Taiwan.
NSF EAPSI corals and sites. Pocillopora acuta colonies at Outlet reef (top) and Wanglitung reef (bottom) near Kenting, Taiwan.

I also was involved in projects funded by the Florida Department of Environmental Protection that investigated the gene expression of diverse Caribbean coral species in response to infection with the Stony Coral Tissue Loss Disease (SCTLD), the results of which are published here.

Other projects

  • Physiology and transcriptome responses of Pocillopora corals to antibiotic microbiome suppression - GitHub Link
  • Meta-analysis of Pocillopora RNAseq datasets in the NCBI SRA - GitHub Link
  • Genomic species delimitation of Pocillopora corals in the eastern tropical Pacific of Panama
  • Coral conservation genetics for reef restoration workshop, in partnership with Raising Coral Costa Rica - Course Website
Pocillopora corals are ecosystem engineers in the ETP. A single large Pocillopora colony growing on Isla Champion in the Galápagos Islands, Ecuador.
Pocillopora corals are ecosystem engineers in the ETP. A single large Pocillopora colony growing on Isla Champion in the Galápagos Islands, Ecuador.