Table of Contents

• Coverage
• Dataset Description
  • Methods & Sampling
  • Data Processing Description
  • BCO-DMO Processing Description
• Data Files
• Related Publications
• Related Datasets
• Parameters
• Project Information
• Funding

Sampling was conducted at several locations: South Korea, Japan, USA, European coastlines, Argentina, and Chile.

At each site, we collected approximately 20 individuals at least 1 meter apart from natural and artificial substrata outside of obvious aquacultural infrastructure to target naturally-settled spat. The two exceptions were in Chile, which were a mix of aquacultural (n=17) and feral (n=3) samples collected from the same estuary (Estero Tongoy), and New Zealand, where oysters were naturally settled within aquaculture farms. Shells were pulled by hand off of hard substrata. Whole or mantle tissue was preserved in 95% ethanol and shipped to Charleston, South Carolina (USA) for DNA extraction using Macherey-Nagel Nucleospin Tissue kits, using the manufacturer's instructions.

To generate libraries for RADseq (restriction-site associated DNA sequencing), we digested gDNA with two restriction enzymes, EcoRI and MseI, and ligated adaptors containing unique 8 to 10 bp barcodes to the digested DNA of each individual. The products were then PCR amplified in two independent reactions with standard Illumina primers. All amplicons were pooled and shipped to the University of Texas Genomic Sequencing and Analysis Facility or the Tufts University Core Facility, which used Pippin Prep® to isolate the 300 – 450 bp fraction. This fraction was then single-read sequenced (100 or 150 basepairs) with Illumina Novaseq, HiSeq 2500 and/or HiSeq 4000 machines. We used custom scripts to demultiplex into sample-specific FASTQ-formatted files.

These data are the demultiplexed files from Illumina sequencing.

- Imported original file "meta_forBIODMO.csv" into the BCO-DMO system.
- Created column for collection date in YYYY-MM format.
- Saved final file as "958631_v1_m_gigas_sra.csv".

NSF abstract:

During the 20th century, the Pacific oyster Crassostrea gigas was deliberately introduced from its native range of coastal Asia to the estuaries of six continents. While the introduced Pacific oysters are widely aquacultured and thus can generate local economic wealth, they sometimes outcompete native oysters, and can carry microbial, animal and plant hitchhikers that negatively impact local economies and the ecological functioning of local estuaries. This study comprehensively assesses the pathways and sources of Pacific oyster introductions using a worldwide, population genetic survey. Simultaneously, the study also assesses the pathways and source of one hitchhiking protist (Haplosporidium nelsoni) that causes the disease MSX (multinucleated sphere X) in the Virginia oyster (Crassostrea virginica) along the eastern seaboard of the United States. One goal of this research is to generate management strategies that combat the negative impacts of the Pacific oyster and its associated invaders, and minimize future invasions. A second goal is to minimize some uncertainty about the population biology of the devastating Haplosporidium parasite, and thus, increase confidence of policy makers who are managing shellfish health, restoration and commerce. By quantifying the pathways and sources of C. gigas, this project may inform strategies to combat negative impacts of C. gigas and its associated invaders, as well as minimize future invasions. Moreover, quantifying dispersal within and among populations of H. nelsoni along the US East Coast will provide perspective on the effectiveness of regional biosecurity measures in preventing the ongoing dispersal of this destructive pathogen via aquaculture. In addition, the project lends itself well to programs that foster critical thinking and research experience among both undergraduate and K-12 students. The project provides opportunities for 6-9 undergraduates to perform research, includes a 2-day workshop on bioinformatics for the wider undergraduate community, and facilitates ongoing opportunities for K-12 students to participate in citizen-science research.

There is a wealth of information on the source, pathways and vectors of C. gigas based largely on historical documents but no study has comprehensively tested whether these historical accounts are correct using a worldwide, population genetic survey. Using >14K single-nucleotide polymorphisms (SNPs) from 41 populations across five continents a high level of spatial genetic differentiation was found within the native range and differences in source populations among non-native regions. Preliminary genetic data indicated that the parasitic protist, Haplosporidium nelsoni arrived with C. gigas imports to the US Atlantic coastline and then infected the native C. virginica, however the native source populations, the pathways and vector from which H. nelsoni arrived remain unknown. This project couples high-throughput sequencing technologies and Approximate Bayesian Computing (ABC)-based models to answer the following: What are the population genomic patterns among C. gigas from native and non-native regions? What are the population genomic patterns of Haplosporidium nelsoni among Asian and North American Crassostrea gigas and eastern North American C. virginica? What were the source populations and invasion pathways of C. gigas and H. nelsoni? Identifying source locations, pathways and vectors of introduction of C. gigas will provide researchers with a null-model of invasion history for dozens of other non-native species that were transported with C. gigas. Currently, there are no verified 'vector maps' for historical shipments of C. gigas that are similar to those generated from modern-day or historical shipping records.

This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.