Using existing habitat datasets and natural-history traits, we created a Habitat Suitability Index (HSI) model in ArcGIS to determine the distribution of suitable habitat for harvested clams in Yaquina Bay. Existing habitat datasets were used to interpolate value estimates throughout the bay for the four input habitat variables used in the model (sediment % fines, bathymetry, salinity, and burrowing shrimp presence). Natural history traits (derived from literature) were then used to assign binary suitability values to each habitat variable for each species. The suitability sum of these variable layers then produced an overall HSI value of 0-4 (low-high). To validate this model, we used existing bivalve (presence/absence) data to calculate presence probabilities. Included in this dataset are these bivalve data, along with the habitat estimates and suitability values produced by our model. This dataset is associated with the following publication: Lewis, N., E. Fox, and T. DeWitt. Estimating the distribution of harvested estuarine bivalves with natural-history-based habitat suitability models... ESTUARINE, COASTAL AND SHELF SCIENCE. Elsevier Science Ltd, New York, NY, USA, 219: 453-472, (2019).

PURPOSE: Establishing efficient, non-destructive sampling methods for clam population assessments. DESCRIPTION: In the Gulf of St. Lawrence (GSL) Management Region, clam assessments are uncommon due to limited resources and the labour-intensive nature of sampling clam beds. Furthermore, clam assessments typically rely on destructive sampling that disturbs sediment and removes animals from their habitat. Establishing efficient, non-destructive sampling methods for clam population assessments can reduce the impact of scientific sampling on these habitats and provide for more efficient monitoring. In this study, we tested the idea that visually observing siphon holes on the sediment surface could predict the presence, number, and size of soft-shell clams across different sites in the southern GSL. Siphon holes reasonably predicted the presence, number, and size/biomass of soft-shell clams in most, but not all, sites. Thus, in many habitats in the GSL, siphon holes can be used for population assessments, providing a powerful tool to enhance Science advice to fisheries managers. Data was collected at the following sites: * Maisonnette, Parc Maisonnette, Maisonnette, New Brunswick, Canada * Kouchibouguac, Loggiecroft wharf, Kouchibouguac National Park, New Brunswick, Canada * Shemogue, Amos Point Road, Little Shemogue, New Brunswick, Canada * Powell's Cove, Powell's Point Provincial Park, Little Harbour, Nova Scotia, Canada PARAMETERS COLLECTED: - Clam abundance - Clam biomass (total sample) - Clam size (length, weight) - Siphon hole abundance - Siphon hole size - Siphon hole characterization (i.e., identification of actual clam based on shape) - Seawater temperature - Sediment grain size - Sediment organic content (%) - Sediment relative moisture content (%) NOTES ON QUALITY CONTROL: Original data entry by Jillian Hunt and/or Isabelle Brennan. Data checked and validated prior to analysis by Jeff Clements. Data further checked and validated prior to publication by Amélie Robichaud. PHYSICAL SAMPLE DETAILS: No physical samples retained. - Clam samples returned back to original habitat after measuring and weighing in the field. - Sediment core samples stored in walk-in freezer and discarded after processing and analysis. SAMPLING METHODS: i. Identifying, counting, weighing, and measuring (with calipers) clams ii. Identifying, counting, and measuring (with calipers) clam siphon holes iii. Seawater temperature monitoring via data loggers iv. Sediment grain size, organic content, and moisture content analysis USE LIMITATION: To ensure scientific integrity and appropriate use of the data, we would encourage you to contact the data custodian.

A barrier island seagrass habitat suitability index (HSI) model was developed for the Alabama barrier island restoration assessment at Dauphin Island. Shoal grass (Halodule wrightii) was selected as the representative species for seagrass community near Dauphin Island waters since H. wrightii is the dominant species (>62%) of seagrass communities in this area due to its rapid growth and tolerance to a wide range of salinity. Five water quality and morphological variables were selected and their relationships with habitat suitability were developed and incorporated into the seagrass HSI model for Dauphin Island restoration assessment: 1) mean salinity during the summer growing season, 2) mean temperature during the growing season, 3) annual mean water depth, 4) mean total suspended solid/turbidity during the growing season, and 5) relative wave exposure index (REI). The final HSI score was calculated using the weighted geometric mean of the suitability scores of these individual variables. The seagrass HSI model was calibrated and validated using field data from National Park Service (NPS) Gulf Coast Inventory and Monitoring Network (GULN). Then, the seagrass HSI model was used to assess seagrass habitat suitability changes with and without restoration under future storminess and sea level (SL) conditions. The barrier island restoration actions being assessed include beach and dune restoration, marsh restoration, and placement of sand in the littoral zone. The storminess bins included realizations with a “medium” storminess, which included 1 to 3 storms over a 10-year period (that is, ST2) and a “high” storminess, which included 4 to 5 storms over an equal period (that is, ST3). The two future sea levels included a SL of 0.3 m (that is, SL1) and a SL of 1.0 m(that is, SL3) above the contemporary SL. Specifically, the medium storminess was paired with the 0.3 m above the contemporary SL (that is, ST2SL1) and the “high” storminess bin was paired with the 1.0 m above the contemporary SL (that is, ST3SL3). To account for intertidal marsh vertical accretion as a component of marsh morphology evolution, two scenarios were included in modeling: the U.S. Army Corps of Engineers (USACE) high and intermediate SLR curves in which marsh kept pace with SLR through accretion (1 cm/yr) through 2022 under high SLR curve whereas marsh kept pace with SLR by accretion for the entirety of the USACE intermediate curve. Inputs of water quality conditions under future storminess and sea level conditions were provided by the CE-QUAL-ICM model that was coupled with a geomorphology model and a hydrodynamic model. The relative wave exposure index (REI) for each scenario was estimated from wind climatology data and fetch and USGS Coastal National Elevation Database (CoNED) topography and bathymetry digital elevation model (TBDEM) that was updated by the landscape-position habitat model. This data release includes simulation results and metadata of seagrass habitat suitability scores at each spatial unit (grid cell) across the study domain: estuarine waters near Dauphin Island.

The Federal Columbia River Power Supply (FCRPS) Biological Opinion (BiOp) calls for studies that estimate ecological and genetic impacts of hatchery fish on wild populations, and evaluate the effectiveness of hatchery supplementation measures to reduce potentially harmful effects of artificial production to aid recovery through hatchery reform. The FCRPS BiOp further explicitly calls for studies that examine the appropriate role of supplementation and the relationship between supplementation and habitat actions in salmon recovery. A basic premise of supplementation is that artificially produced fish will help develop self-sustaining spawning populations both by increasing current natural production and reestablishing populations in underutilized and recovered habitats. One hatchery reform measure that has been incorporated into many supplementation programs throughout the Columbia River Basin is the use of satellite acclimation facilities to repopulate underutilized habitat. However, the efficacy of these facilities in re-establishing naturally spawning populations and minimizing negative interactions between wild spawners and supplemented fish has not been established. Our studies have involved comprehensive carcass and redd mapping surveys and radio telemetry to examine the role of acclimation sites in homing and spawning of spring Chinook salmon released as part of the Yakima/Klickitat Fisheries Project (YKFP) supplementation program. In addition, we are examining the complex linkages between habitat quality and spawning site selection in supplemented Columbia River populations. These studies involve mapping and assessing habitat distribution and quality relative to supplementation rearing and release facilities, and coupling these findings to ongoing analysis of homing and spawning patterns. Our results have provided unique insights into the process of homing, straying, and spawning site selection, interactions and success of hatchery and wild spawners, and the efficacy of supplementation and acclimation sites in salmon recovery. These studies will help identify appropriate locations for recovery-related supplementation rearing and release facilities (acclimation sites), and ultimately allow us to develop scenario models predicting the spatial distribution of spawning relative to proposed supplementation facilities and available habitat (including future habitat restoration sites). The work is being conducted by Northwest Fisheries Science Center (NWFSC) scientists collaborating with the University of Washington, Yakima Nation, U.S. Geological Survey (USGS), and the Washington Department of Fish and Wildlife (WDFW). Products for this project include annual reports, peer-reviewed publications, presentation of results at local and national meetings, and consultation with the Northwest Regional Office (NWR) and supplementation managers. Comprehensive GIS data of Yakima River Spring Chinook spawners.

To quantify any spatial or temporal variability in cockle densities with respect to in situ GMA biomass in Yaquina Bay, OR, we conducted field surveys during consecutive daytime low tides (<0.46 m MLLW) in both June and August 2014, which provided a comparison between early and late summer. This dataset contains all data collected during those field surveys. This dataset is associated with the following publication: Lewis, N., and T. DeWitt. Effect of Green Macroalgal Blooms on the Behavior, Growth, and Survival of Cockles (Clinocardium nuttallii) in Pacific NW Estuaries. MARINE ECOLOGY PROGRESS SERIES. Inter-Research, Luhe, GERMANY, 582: 105-120, (2017).

To quantify any spatial or temporal variability in cockle densities with respect to in situ GMA biomass in Yaquina Bay, OR, we conducted field surveys during consecutive daytime low tides (<0.46 m MLLW) in both June and August 2014, which provided a comparison between early and late summer. This dataset contains all data collected during those field surveys. This dataset is associated with the following publication: Lewis, N., and T. DeWitt. Effect of Green Macroalgal Blooms on the Behavior, Growth, and Survival of Cockles (Clinocardium nuttallii) in Pacific NW Estuaries. MARINE ECOLOGY PROGRESS SERIES. Inter-Research, Luhe, GERMANY, 582: 105-120, (2017).

Data describes habitat suitability modelling (HSM) results for fish in streams. The data was developed by University of Melbourne through the Melbourne Waterways Research Practice Partnership as part of the development of Melbourne Water’s Healthy Waterways Strategy 2018 (HWS2018). Analysis has been undertaken across the Melbourne Water operating region, where the operating region has been divided into 16,346 sub-catchments. Of these 16,346 subcatchments, 8233 contain Melbourne Water waterways. The results are presented for each of these 8233 reaches for these HWS scenarios:Current: habitat suitability for fish under current conditions (i.e. 2014).Current trajectory: habitat suitability for fish under urbanisation and climate change scenarios if current management approaches continue. Target trajectory: habitat suitability for fish given urbanisation and climate change (as for current trajectory), together with (a) delivery of performance objectives of the Healthy Waterways Strategy and (b) achievement of environmental condition scores as described in the Catchment Programs of the Healthy Waterways Strategy.Results are presented as:Stacked probabilities, i.e. habitat suitability all 13 native fished species added together. These stacked probability values were used in the HWS to provide a fish value score each reach and sub-catchments.Results are also provided for all 22 fish species. Presentation of habitat suitabilty model results for fish from the Healthy Waterways Strategy 2018.Habitat Suitability Model results have been thoroughly reviewed and are considered fit for purpose (i.e. for waterway planning). This data set covers the entire Melbourne Water region with the exception of very small areas close to Port Phillip Bay or Western Port. For example, there are small areas of French Island which are not captured.This data set was created using: 1. Streams dataset for the Healthy Waterways Strategy 2018 (developed by GraceGIS using Melbourne Water layers as inputs), and 2. Results from Habitat Suitability Modelling for the Healthy Waterways Strategy 2018. Further reading: Chee et al. (in development), Habitat Suitability Models, Scenarios and Quantitative Action Prioritisation (using Zonation) for Melbourne Water’s Healthy Waterways Strategy: A Resource Document, University of Melbourne and Melbourne Water for Melbourne Waterways Research Practice Partnership Melbourne Water (in development), Healthy Waterways Strategy Resource DocumentNOTE: Whilst every effort has been taken in collecting, validating and providing the attached data, Melbourne Water Corporation makes no representations or guarantees as to the accuracy or completeness of this data. Any person or group that uses this data does so at its own risk and should make their own assessment and investigations as to the suitability and/or application of the data. Melbourne Water Corporation shall not be liable in any way to any person or group for loss of any kind including damages, costs, interest, loss of profits or special loss or damage, arising from any use, error, inaccuracy, incompleteness or other defect in this data.

This dataset contains juvenile Dungeness crab (Cancer magister) abundance data and associated habitat data from three estuaries in Oregon (Tillamook, Yaquina, and Alsea bays). These data were collected by EPA surveys in 2010-2011. Additionally, this dataset includes areal data on National Wetlands Inventory (NWI) habitat classes within our study areas. This dataset is associated with the following publication: Lewis, N., D. Young, C. Folger, and T. DeWitt. Assessing the Relative Importance of Estuarine Nursery Habitats – a Dungeness Crab (Cancer magister) Case Study. Estuaries and Coasts. Estuarine Research Federation, Port Republic, MD, USA, s12237-020-00821-1, (2020).