16 Habitat Diversity

Description: Species richness was derived from the Northeast Regional Habitat Assessment models for 55 common species sampled by the 2000-2019 spring and fall NEFSC bottom trawl surveys. The joint species distribution model controls for differences in capture efficiency across survey vessels.

Indicator category: Extensive analysis

Found in: State of the Ecosystem - New England (2023), State of the Ecosystem - Mid-Atlantic (2023)

Contributor(s): Chris Haak

Data steward: Laurel Smith

Point of contact: Laurel Smith

Public availability statement: This analysis is based on NEFSC bottom trawl survey data which are publicly available. Please reached out to Laurel Smith with questions.

16.1 Methods

16.1.1 Data sources

Abundance data were extracted from the NEFSC’s SVDBS database using Survdat for 55 fish species regularly sampled on spring and fall NEFSC bottom trawl surveys:

Species included in NRHA Diversity Index:

Common Name Scientific Name
Acadian Redfish Sebastes fasciatus
Alewife Alosa pseudoharengus
American Lobster Homarus americanus
American Plaice Hippoglossoides platessoides
American Shad Alosa sapidissima
Atlantic Cod Gadus morhua
Altantic Croaker Micropogonias undulatus
Atlantic Herring Clupea harengus
Atlantic Mackerel Scomber scombrus
Barndoor Skate Dipturus laevis
Black Sea Bass Centropristis striata
Blackbelly Rosefish Helicolenus dactylopterus
Blueback Herring Alosa aestivalis
Bluefish Pomatomus saltatrix
Butterfish Peprilus triacanthus
Chain Dogfish Scyliorhinus retifer
Clearnose Skate Rostroraja eglanteria
Fawn Cusk Eel Lepophidium profundorum
Fourbeard Rockling Enchelyopus cimbrius
Fourspot Flounder Hippoglossina oblonga
Goosefish Lophius americanus
Gulf Stream Flounder Citharichthys arctifrons
Haddock Melanogrammus aeglefinus
Horseshoe Crab Limulus polyphemus
Jonah Crab Cancer borealis
Little Skate Leucoraja erinaceus
Longfin Squid Doryteuthis (Amerigo) pealeii
Longhorn Sculpin Myoxocephalus octodecemspinosus
Northern Searobin Prionotus carolinus
Northern Shortfin Squid Illex illecebrosus
Northern Shrimp Pandalus borealis
Ocean Pout Zoarces americanus
Offshore Hake Merluccius albidus
Pollock Pollachius pollachius
Red Hake Urophycis chuss
Rosette Skate Leucoraja garmani
Scup Stenotomus chrysops
Sea Raven Hemitripterus americanus
Sea Scallop Placopecten magellanicus
Silver Hake Merluccius bilinearis
Smooth Dogfish Mustelus canis
Smooth Skate Malacoraja senta
Spiny Dogfish Squalus acanthias
Spot Leiostomus xanthurus
Spotted Hake Urophycis regia
Striped Searobin Prionotus evolans
Summer Flounder Paralichthys dentatus
Thorny Skate Amblyraja radiata
Weakfish Cynoscion regalis
White Hake Urophycis tenuis
Windowpane Flounder Scophthalmus aquosus
Winter Flounder Pseudopleuronectes americanus
Winter Skate Leucoraja ocellata
Witch Flounder Glyptocephalus cynoglossus
Yellowtail Flounder Myzopsetta ferruginea

Data were converted to presence/absence for species richness modeling.

16.1.2 Data analysis

16.1.2.1 Species Richness

Estimated species richness is the number of unique species expected to be observed in NEFSC bottom trawl surveys conducted in a given ecological production unit (EPU) and year, based on a fitted joint-species distribution/habitat suitability model (considering only the 55 commonly-occurring species listed above).

16.1.2.2 Model Fitting

A spatiotemporal joint species distribution model was fitted to n=13231 observations of presence/absence in the Spring and Fall NEFSC bottom trawl surveys for the years 2000-2019, using the Community Level Basis Function Model (CBFM) framework with a binomial error distribution and logistic link function. The probability of presence was modeled as a function of environmental predictor variables (using smooth terms), a vessel effect (factor) to account for changes in sampling gear, as well as spatiotemporal (Lat, Lon, Month) and temporal (Year) random effects, which were estimated hierarchically through a set of species-common basis functions. The model thus controls for differences in capture efficiency across survey vessels, permitting predictions on a common scale (here calibrated to the RFV Albatross IV).

16.1.2.3 Environmental Covariates

Covariate values (i.e., environmental parameters) corresponding to the approximate location (and time, when applicable) of each observation (i.e., tow) were extracted from the following sources: Monthly mean surface and bottom temperature, surface and bottom salinity, and sea surface height anomaly were obtained from the GLORYS12V1 reanalysis (Jean-Michel et al. (2021a)), as were annual minimum and maximum surface and bottom temperatures.

Monthly mean underwater optical parameters, including the intensity (photosynthetically active radiation - PAR) and spectral composition (hue angle) of downwelling light at mid-water column, were estimated from remote sensing data, following the methods of Z.-P. Lee et al. (2005) and Z. Lee et al. (2022), respectively.

Hydrodynamic stress near the seabed (95th quantile) was obtained from the USGS Sea Floor Stress and Sediment Mobility database (Dalyander et al. 2012).

Annually-integrated chlorophyll was obtained from the Oceancolour-CCI (version 5) release (https://www.oceancolour.org/).

Bathymetric position index (BPI), benthic structural complexity, and sediment type data were estimated following the methods described at: https://www.conservationgateway.org/ConservationByGeography/NorthAmerica/UnitedStates/edc/reportsdata/marine/namera/namera/Pages/default.aspx/

16.1.2.4 Estimating Richness

Simulating from the fitted model, we generated 100 random draws of “joint” predictions of the species assemblage observed in the survey, taking into account species residual covariances (see Wilkinson et al. (2021) for additional details). We used these to produce estimates of the mean species richness (and corresponding 95% prediction intervals) across all observations within each ecological production unit (EPU) for each modeled year (2000-2019).

16.1.3 Data Processing

The Habitat Diversity indicator was formatted for inclusion in the ecodata R package with the code found here.

catalog link https://noaa-edab.github.io/catalog/habitat_diversity.html

References

———, et al. 2021a. “The Copernicus Global 1/12° Oceanic and Sea Ice GLORYS12 Reanalysis.” Frontiers in Earth Science 9. https://doi.org/10.3389/feart.2021.698876.
Lee, Zhong-Ping, Miroslaw Darecki, Kendall L. Carder, Curtiss O. Davis, Dariusz Stramski, and W. Joseph Rhea. 2005. “Diffuse Attenuation Coefficient of Downwelling Irradiance: An Evaluation of Remote Sensing Methods.” Journal of Geophysical Research: Oceans 110 (C2). https://doi.org/https://doi.org/10.1029/2004JC002573.
Lee, Zhongping, Shaoling Shang, Yonghong Li, Kelly Luis, Minhan Dai, and Yongchao Wang. 2022. “Three-Dimensional Variation in Light Quality in the Upper Water Column Revealed with a Single Parameter.” IEEE Transactions on Geoscience and Remote Sensing 60: 1–10. https://doi.org/10.1109/TGRS.2021.3093014.
Wilkinson, David P., Nick Golding, Gurutzeta Guillera-Arroita, Reid Tingley, and Michael A. McCarthy. 2021. “Defining and Evaluating Predictions of Joint Species Distribution Models.” Methods in Ecology and Evolution 12 (3): 394–404. https://doi.org/https://doi.org/10.1111/2041-210X.13518.