Table of Contents

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

Samples of Carcinus maenas (urn:lsid:marinespecies.org:taxname:107381) were collected between May 2022 and Aug 2022 from Massachusetts waters. 

Extractions were performed with an NEB Monarch HMW DNA Extraction Kit for Cells & Blood (May runs; low success) or a Circulomics Nanobind Tissue Big DNA kit (June and August runs; good success). Library prep was performed with a Oxford Nanopore Cas9 sequencing kit and custom Cas9 probes targeting putative inversion regions. May and June runs used the same first-round set of probes, while August runs used an updated second-round set of probes. Probe sequences are included in the supplemental file and can be cross-referenced using the probe_set value, though targeting is imperfect so much of the data simply reflect non-targeted genome sequencing. Libraries were sequenced on a single flowcell of an Oxford Nanopore MinION mk1c. For each round of sequencing (May, June, and August), the same library was run twice for 24 hours each time, with a flowcell flush at 24 hours. The run_day value captures this, listing this pre- and post-flush runs as run_days 1 and 2, respectively, for each single sample.

Minimal initial processing with standard Oxford Nanopore MinKNOW software (v22.03.06) was used to convert native fast5 files into fastq format for downstream processing. Only the fastq files in the "pass" bin were shared to the SRA. The MinKNOW software includes the following subpackage versions: MinKNOW core v5.0.0, Guppy v6.0.7, Bream v7.0.9, and Script Configuration v5.0.8.

- Imported "BCODMO_MinION_metadata_NSF-1850996.csv" into BCO-DMO system
- Converted "Collection_date" and "sequencing_date" to ISO 8601 format
- Exported resource as "949666_v1_longread_seq_metadata.csv"

Accepted species identifier confirmed on 2025-01-29.

NSF Award Abstract: 
Marine invasive species pose a serious and ongoing risk to ocean ecosystems and the economies that rely on them. Understanding how such species adapt rapidly to new environments is key to preventing and managing invasions. Traditionally, the focus has been on inherent traits and flexibility of an invasive species, ignoring the potential for evolutionary change after introduction. However, recent research has shown that some marine species may evolve specific genomic features which allow highly efficient selection over as little as a single generation. This project tests the importance of genomic traits in allowing marine invasive species to survive and thrive on new shores. Its focus is on the high-impact invasive European green crab, which has spread over 1,500 km of the West Coast of North America since 1989 and has very recently begun expanding into the Salish Sea. This project tracks the earliest stages of green crab invasion into a new environment where the species is predicted to have substantial ecological and economic impacts. Genetic differences are followed over time and space across the entire West Coast, with a focus on crabs found in the Salish Sea where the species is currently expanding. Genetic data is complemented by oceanographic modeling to predict the spread of green crabs into the Salish Sea and across the West Coast. Finally, targeted sequencing and prior sampling are used to probe the genomic traits underlying these changes and determine if the same traits have played a role in the species' invasive success on other shores. Sampling for this project is conducted by Washington Sea Grant's Crab Team, an expansive outreach and monitoring program powered largely by hundreds of volunteers who monitor green crabs across 3,000 miles of coastline in the Salish Sea. The results of this project are shared with these volunteers and other stakeholders and is used to inform trans-boundary green crab management and spread prediction on the West Coast.

Recent work has hypothesized that genomic architecture, which has been increasingly discovered to play a role in local adaptation, may also be key to a species' ability to adapt quickly when gene flow is high. This project integrates multiple approaches to track the speed and dynamics of adaptation-with-gene flow across a thermal gradient in an explicit oceanographic context using the invasive European green crab (Carcinus maenas). Prior work in this system identified a suite of genes that appear to constitute balanced polymorphisms whose allele frequencies correlate strongly with site temperature against a homogeneous neutral genetic background. This project has three main goals: 1) To examine fine-scale selection to temperature over a comprehensive spatial and temporal data set comprising most of the species' history on the West Coast, 2) To track the expanding range front in the Salish Sea, comparing the genetic trajectory of individuals at the range edge with oceanographic modeling of dispersal, and 3) To characterize the genomic regions surrounding putative balanced polymorphisms and examine the ubiquity of their association with temperature across globally replicated populations. This coupled evolutionary oceanography approach represents an unprecedented test of the speed and nature of rapid adaptation in a highly dynamic natural marine environment.

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.