Fisheries Bycatch, Vessel Strikes and Other Sources of Human-Caused Mortality

Background

Quantifying human-caused mortality and serious injury (M/SI) is integral to producing marine mammal stock assessments. Sources of human-caused M/SI include fishery bycatch, marine debris entanglements, shootings, acoustic trauma, and vessel strikes.

  1. We use fishery observer data to provide annual estimates of marine mammal bycatch in fisheries along the U.S. West Coast (Carretta 2024), and to identify environmental factors and fishing gear improvements to reduce bycatch risk. We work with the Pacific Offshore Take Reduction Team that includes fishermen, conservation organizations, and scientists, to evaluate bycatch trends in the U.S. West Coast swordfish gillnet fishery and implement strategies for bycatch reduction (Barlow and Cameron 2003). Our involvement in bycatch reduction and assessment led to the introduction of acoustic pingers into the swordfish gillnet fishery in the 1990s, which resulted in the elimination of beaked whale bycatch and large reductions in the bycatch of other marine mammal species.

  2. Other sources of human-caused mortality and serious injury include vessel strikes, shootings, marine debris entanglements Carretta et al. 2024, and acoustic trauma (St.Leger and Danil 2011)

Annual MMPA SAR requirements to enumerate human-caused M/SI

Annually, collating, evaluating, and summarizing human-caused M/SI is required to 1) produce an annual human-caused M/SI Technical Memorandum and 2) update SARS. The most current M/SI data file, where new records and determinations are entered and previous records edited, is HCMSI_Records_SWFSC_Main.xlsx, housed in the public SWFSC/MSI-data GitHub repository (note that since this repository is public, care is required to ensure that all PII is eliminated from records as they are entered in this data sheet).

Data sources / contacts for human-caused M/SI data include:

  1. States (CA sea lion removals under Sec. 120 of the MMPA): Robert.C.Anderson@noaa.gov and Nancy.Young@noaa.gov receive and share these data annually

  2. NMFS Regional Offices and Science Centers (all taxa): Allison.Henry@noaa.gov (NEFSC - Atl whales), Justin.Greenman@noaa.gov (WCR - all taxa), Lauren.Saez@noaa.gov (WCR - large whales), Kristin.Wilkinson@noaa.gov (NWFSC - all taxa), Nancy.Young@noaa.gov (AFSC - all taxa), Amelia.Brower@noaa.gov (AFSC - all taxa), Amanda.Bradford@noaa.gov (PIFSC - U.S. west coast pinnipeds that show up in HI longlines), Kayleigh.Somers@noaa.gov (NWFSC - all taxa NW groundfish fisheries), Elise.Kohli@noaa.gov (SWFSC - research takes). See also below for contacts for CDGN and set gillnet bycatch from PacFin.

  3. Cross-center review: Allison.Henry@noaa.gov (NEFSC - large whales), Nancy.Young@noaa.gov and Amelia.Brower@noaa.gov (AFSC - pinnipeds and small cetaceans).

The annual human-caused M/SI report is produced in the format of Carretta et al. 2024, and traditionally includes the most recent five years of available data. To generate an annual report, you will use R scripts and an R Markdown file housed in the SWFSC/MSI-report repository (accessible to all NOAA Github Enterprise users) to produce an automated report based on the HCMSI_Records_SWFSC_Main.xlsx file. Detailed instructions are provided within the SWFSC/MSI-report repository, and include these main steps:

  1. Run ‘SeriousInjuryExtract.R’ to data mine HCMSI_Records_SWFSC_Main.xlsx. Running this script produces an RData file, which interacts with the steps 2 and 3.

  2. Run ‘AppendixTable.R’ to produce Appendix 1 as a DOCX file for the report.

  3. Run R Markdown file ‘HCM_SI_Report.Rmd’ to produce the main body of the annual report as a DOCX file, which is edited for format and collated with Appendix 1 for publication.

Bycatch Estimation in CA Swordfish gillnet fishery

This fishery is scheduled for phase-out in 2027, stay tuned. Only a handful of vessels participating. Data is housed at PacFin and requires a login and a data confidentiality agreement. The files used for data manipulation and analysis are in the directory “C:/CARRETTA/Github/DGNBycatch” (R-Studio project, not a package). The entire workflow including data download, variable selection, and bycatch estimation is found in the HTML file: “C:/Carretta/GitHub/DGNBycatch/R/DGN_Bycatch_Workflow.html”, Which is generated via “C:/Carretta/GitHub/DGNBycatch/R/DGN_Bycatch_Workflow.RMD”

People to know: charles.villafana@noaa.gov (Observer program). He knows all the PacFin folks housing the data, including: Ryann Turcotte RTurcotte@psmfc.org , and Robert Ryznar RRyznar@psmfc.org

SeriousInjury R-Package and Shiny App

A Shiny Tool and R-Package used to assess the probability of death for large whale injuries. [It is under consideration for use] as a NMFS National Policy for assessing large whale injuries. Based on the Carretta and Henry (2022) publication. Two identical Github repositories exist for the SeriousInjury package: https://github.com/SWFSC/SeriousInjury https://github.com/JimCarretta/SeriousInjury

Once installed, the function SeriousInjuryTutorial( ) opens an HTML window. You can also run the Shiny App, based on instructions in the tutorial.

Caption