Abstract:

The Regional Ocean Modeling System (ROMS) was used to simulate hydrodynamics in the Atlantic Ocean, the Caribbean Sea and the Gulf of Mexico for the period 2007 to 2017. The circulation fields drove a particle tracking simulation and quantified the transport connectivity for the study area. The model domain spans the northwest Atlantic with ~7 km horizontal grid spacing and 36 vertical layers and the bathymetry was generated using 1-min gridded GEBCO (General Bathymetric Chart of the Oceans) data and smoothed using Sikirić et al. (2009) methodology to remove large gradients that may lead to numerical pressure gradient errors for the model. The model used fourth-order centered advection using k-kl mixing coefficients (corresponding to Mellor-Yamada Level 2.5) with the generic length scale vertical mixing scheme (Warner et al. 2005). The model was configured to conserve volume with a free-surface Chapman condition (Chapman 1985), a Flather condition for 2D momentum (Flather 1976), and the Orlanski-type radiation condition (Orlanski 1976) for 3D momentum and tracers (Marchesiello et al. 2001; Zeng et al. 2015a) at its only open boundary to the east. The boundary values of ocean states were derived from the daily global Hybrid Coordinate Ocean Model (HYCOM) product. The surface forcing used in the ROMS simulation was derived from the European Center for Medium-Range Weather Forecast (ECMWF) reanalysis product with 0.125-degree grid spacing every three hours. The model was initialized with daily HYCOM output and ran from January 1, 2007, to December 14, 2017. This dataset supports the publication: Zeng, X., Adams, A., Roffer, M., & He, R. (2018). Potential connectivity among spatially distinct management zones for Bonefish (Albula vulpes) via larval dispersal. Environmental Biology of Fishes, 102(2), 233–252. doi:10.1007/s10641-018-0826-z.

Suggested Citation:

Zeng, Xiangming, Ruoying He, and Joseph Zambon. 2020. Dataset for: Potential connectivity among spatially distinct management zones for Bonefish (Albula vulpes) via larval dispersal. Distributed by: GRIIDC, Harte Research Institute, Texas A&M University–Corpus Christi. doi:10.7266/S4ZP4C7F

Publications:

Zeng, X., Adams, A., Roffer, M., & He, R. (2018). Potential connectivity among spatially distinct management zones for Bonefish (Albula vulpes) via larval dispersal. Environmental Biology of Fishes, 102(2), 233–252. doi:10.1007/s10641-018-0826-z

Purpose:

The Regional Ocean Modeling System (ROMS) was used to simulate hydrodynamics in the Northwest Atlantic Ocean region from 2009 to 2015. The resulting circulation fields are applied to drive particle tracking simulation to quantify transport connectivity.

Data Parameters and Units:

Lon (degree), lat (degree), s_rho (vertical coordinate), time (day), sea surface height (m), temperature (celsius); salinity; u_eastward (m/s), v_northward (m/s), ubar (vertically averaged velocity, m/s); vbar (vertically averaged velocity, m/s) The values of the s-scoordinate parameters are the following: N=36 theta_s=7 theta_b= 0.1 Vtrans= 2 Vstretch=2 Tcline=200

Methods:

Open boundary conditions are obtained from GOFS3.0 HYCOM+NCODA Global 1/12 degree Analysis available at https://www.hycom.org/dataserver/gofs-3pt0/reanalysis and https://www.hycom.org/dataserver/gofs-3pt0/analysis For more detail methods and model settings, please refer to the "Materials and Methods" section in the associated publication Zeng et al., 2018.

Provenance and Historical References:

Chapman DC (1985) Numerical Treatment of Cross-Shelf Open Boundaries in a Barotropic Coastal Ocean Model. J Phys Oceanogr 15:1060–1075. https://doi.org/10.1175/1520-0485 Flather RA (1976) A tidal model of the north-west European continental shelf. Memoires Societe Royale des Sciences de Liege 10:141–164 Marchesiello P, McWilliams JC, Shchepetkin A (2001) Open boundary conditions for long-term integration of regional oceanic models. Ocean Model 3:1–20. https://doi.org/10.1016/S1463-5003(00)00013-5 Orlanski I (1976) A simple boundary condition for unbounded hyperbolic flows. J Comput Phys 21:251–269. https://doi.org/10.1016/0021-9991(76)90023-1 Sikirić MD, Janeković I, Kuzmić M (2009) A new approach to bathymetry smoothing in sigma-coordinate ocean models. Ocean Model 29:128–136. https://doi.org/10.1016/j.ocemod.2009.03.009 Warner JC, Sherwood CR, Arango HG, Signell RP (2005) Performance of four turbulence closure models implemented using a generic length scale method. Ocean Model 8:81–113. https://doi.org/10.1016/j.ocemod.2003.12.003 Zeng X, Li Y, He R, Yin Y (2015a) Clustering of Loop Current patterns based on the satellite-observed sea surface height and self-organizing map. Remote Sensing Letters 6:11–19. https://doi.org/10.1080/2150704X.2014.998347

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