Design and Parameterization of the Chesapeake Bay Atlantis Model: A Spatially Explicit End-to-End Ecosystem Model Thomas F. Ihde, Isaac C. Kaplan, Elizabeth A. Fulton, Iris A. Gray, Mejs Hasan, David Bruce, Ward Slacum, and Howard M. Townsend U.S. Department of Commerce National Oceanic and Atmospheric Administration National Marine Fisheries Service NOAA Technical Memorandum NMFS-F/SPO-166 September 2016 Design and Parameterization of the Chesapeake Bay Atlantis Model: A Spatially Explicit End-to-End Ecosystem Model Thomas F. Ihde1, Isaac C. Kaplan2, Elizabeth A. Fulton3, Iris A. Gray2, Mejs Hasan4, David Bruce4, Ward Slacum5, and Howard M. Townsend4 1NOAA Chesapeake Bay Office, 410 Severn Avenue, Suite 207A, Annapolis, MD 21403; [email protected] 2Conservation Biology Division, Northwest Fisheries Science Center, National Marine Fisheries Service, NOAA, 2725 Montlake Blvd E, Seattle, WA 98112 3Commonwealth Scientific and Industrial Research Organization, Marine and Atmospheric Research, GPO Box 1538, Hobart, Tasmania 7001, Australia 4NOAA Chesapeake Bay Office/Cooperative Oxford Laboratory, 904 South Morris Street, Oxford, MD 21654 5Oyster Recovery Partnership, 1805A Virginia Street, Annapolis, MD 21401 NOAA Technical Memorandum NMFS-F/SPO-166 September 2016 U.S. Department of Commerce Penny S. Pritzker, Secretary National Oceanic and Atmospheric Administration Kathryn D. Sullivan, Administrator National Marine Fisheries Service Eileen Sobeck, Assistant Administrator for Fisheries Recommended citation: Ihde, T. F., I. C. Kaplan, E. A. Fulton, I. A. Gray, M. Hasan, D. Bruce, W. Slacum, and H. M. Townsend. 2016. Design and parameterization of the Chesapeake Bay Atlantis Model: A spatially explicit end-to-end ecosystem model. U.S. Dept. of Commer., NOAA. NOAA Technical Memorandum NMFS-F/SPO-166, 145 p. Copies of this report may be obtained from: NOAA Chesapeake Bay Office 410 Severn Avenue, Suite 207A Annapolis, MD 21403 Or online at: http://spo.nmfs.noaa.gov/tm/ ii Table of Contents List of Figures ................................................................................................................................. v List of Tables ................................................................................................................................ vii Executive Summary ....................................................................................................................... xi Acknowledgments........................................................................................................................ xiv Introduction ..................................................................................................................................... 1 Model Extent and Design................................................................................................................ 3 Projection Years .............................................................................................................................. 6 Physical Model................................................................................................................................ 7 Water Flux, Temperature, and Salinity ....................................................................................... 7 Nutrient and Sediment Inputs ..................................................................................................... 9 Biological Model .......................................................................................................................... 14 Nutrients .................................................................................................................................... 14 Primary Production ................................................................................................................... 15 Invertebrates .............................................................................................................................. 17 Vertebrates ................................................................................................................................ 19 Predation ................................................................................................................................... 20 Spawning and Recruitment ....................................................................................................... 21 Habitat Associations ................................................................................................................. 22 Model Calibration ......................................................................................................................... 24 Model Performance ....................................................................................................................... 24 Initial Calibration: No Fishing .................................................................................................. 24 Model Application ........................................................................................................................ 26 TMDL Scenario ........................................................................................................................ 26 TMDL with expected temperature increase .............................................................................. 26 Discussion ..................................................................................................................................... 27 Current and Future Work .......................................................................................................... 28 Figures 8a–10e and Tables ............................................................................................................ 29 Literature Cited ............................................................................................................................. 88 Appendix A: Map Information ................................................................................................... 104 Chesapeake Bay Atlantis Model ............................................................................................. 104 iii Construction Log for Dynamic Boxes (24 AUG 2010) .......................................................... 104 Bathymetry Metadata .............................................................................................................. 114 Sediment Distribution Metadata ............................................................................................. 114 Appendix B: Biological Processes Modeled in Atlantis ............................................................. 115 Appendix C: Vertebrate Life History ......................................................................................... 117 Fish .......................................................................................................................................... 117 Mammals ................................................................................................................................ 118 Reptiles ................................................................................................................................... 119 Birds ........................................................................................................................................ 120 References—Life History ........................................................................................................... 123 Appendix D: Diets ...................................................................................................................... 133 Fish .......................................................................................................................................... 133 Mammals ................................................................................................................................ 137 Reptiles ................................................................................................................................... 137 Birds ........................................................................................................................................ 138 Invertebrates ............................................................................................................................ 139 References—Diets ...................................................................................................................... 141 iv List of Figures 1a. Spatial structure of CAM. The model consists of 97 irregular polygons determined by salinity, depth, bottom type (mainstem only), and management boundaries. ..................... 4 1b. Detailed river structure of CAM ............................................................................................... 5 2. Vertical structure of CAM ......................................................................................................... 6 3. Chesapeake Bay Water Quality Model (fine-scale cells) superimposed on Atlantis model polygons (yellow) (a), and Atlantis model polygons superimposed on Chesapeake Bay Water Quality Model (b). .................................................................................................... 8 4. Chesapeake Bay 2003 segmentation scheme (78 segments) ................................................... 10 5. Nitrogen inputs for years 1991–2000, as specified by Chesapeake Bay Phase 5.3 Community Watershed model. For the Atlantis simulations presented here, values