Grant: 20-017R
Project Title: Leveraging Next-Generation Sequencing to Identify Genetic Connectivity and Develop Novel Genetic Markers for Gulf of Mexico Loggerheads
Project Manager: Ian Silver-Gorges
Organization: Florida State University (Research and Educational Institute)
Grant Amount: $19,573.50
Completion Date: 2022-06-28
Summary: Sea turtle Management Units (MUs) are not totally isolated from one another, and management plans must account for the scale of demographic isolation, and connectivity, between MUs. Current knowledge suggests that Gulf of Mexico (GoM) loggerheads are split into four MUs based on mitochondrial DNA. Sharing of two primary haplotypes among MUs hinders our ability to investigate the scale of connectivity between the GoM MUs. Microsatellites, highly variable repeating units found throughout the nuclear genome, do not suggest structuring at or below the scale of the GoM for loggerheads. It is unclear if the lack of nuclear structuring found in GoM loggerheads is due to inadequate marker resolution, or to biological processes (such as male-mediated gene flow). The four GoM MUs range in abundance and differ in their vulnerability to anthropogenic threats. Thus, it is critical that we determine the scale of genetic connectivity in GoM loggerheads. This project will develop new genetic markers for GoM loggerheads, nuclear single nucleotide polymorphisms (SNPs), that have the power to determine fine-scale population structure. Our overarching goals are to examine population structuring in GoM loggerheads as suggested by SNP data, and to compare our results to those of previous studies in order to refine our understanding of genetic connectivity in GoM loggerheads. Our development of SNPs will offer new critical insight into the population structure of GoM loggerheads, with potential for applications in other regions and species, and the development of markers for population assignment.
Results: We have made substantial progress towards completing this project. The PI travelled to the University of Massachusetts in February 2022 to assist with RAD library preparation. The library was sent for sequencing in March 2022, and the data were received in mid-April 2022. We are currently in the process of data QAQC. Once this is completed, we will be able to ask for additional sequencing (if necessary) or continue with the analysis pipeline developed by the Komoroske Lab. We expect analysis to be completed by late summer 2022 at the latest, and a publication of our findings to be prepared for submission to a peer-reviewed Journal in early 2023.